https://launchpad.net/ubuntu/+source/python-pysam/0.15.2+ds-2build1/+build/17940056 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-065 4.4.0-165-generic #193-Ubuntu SMP Tue Sep 17 17:45:45 UTC 2019 aarch64 Buildd toolchain package versions: launchpad-buildd_178 python-lpbuildd_178 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 20 Oct 21:32:44 ntpdate[1921]: adjust time server 10.211.37.1 offset -0.026334 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-17940056 --image-type chroot /home/buildd/filecache-default/9d93b4075e16ce7cfbdf01f21507152b0a173b17 Creating target for build PACKAGEBUILD-17940056 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-17940056 Starting target for build PACKAGEBUILD-17940056 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-17940056 'deb http://ftpmaster.internal/ubuntu focal main universe' 'deb http://ftpmaster.internal/ubuntu focal-security main universe' 'deb http://ftpmaster.internal/ubuntu focal-updates main universe' 'deb http://ftpmaster.internal/ubuntu focal-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-17940056 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-17940056 Updating target for build PACKAGEBUILD-17940056 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu focal-security InRelease [66.2 kB] Get:3 http://ftpmaster.internal/ubuntu focal-updates InRelease [66.2 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main arm64 Packages [940 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main Translation-en [505 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe arm64 Packages [8608 kB] Get:8 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5192 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 Packages [68.8 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [41.7 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 Packages [362 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [219 kB] Fetched 16.4 MB in 9s (1902 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.30 perl-modules-5.30 The following packages will be upgraded: base-files binutils binutils-aarch64-linux-gnu binutils-common libapparmor1 libaudit-common libaudit1 libbinutils libcryptsetup12 libgcrypt20 libselinux1 libsemanage-common libsemanage1 lsb-base perl perl-base 16 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 11.6 MB of archives. After this operation, 45.6 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main arm64 base-files arm64 11ubuntu1 [60.4 kB] Get:2 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 perl-modules-5.30 all 5.30.0-7 [2738 kB] Get:3 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libperl5.30 arm64 5.30.0-7 [3740 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 perl arm64 5.30.0-7 [224 kB] Get:5 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 perl-base arm64 5.30.0-7 [1390 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main arm64 libaudit-common all 1:2.8.5-2ubuntu2 [4080 B] Get:7 http://ftpmaster.internal/ubuntu focal/main arm64 libaudit1 arm64 1:2.8.5-2ubuntu2 [38.3 kB] Get:8 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libgcrypt20 arm64 1.8.5-3ubuntu1 [350 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libselinux1 arm64 2.9-2build1 [65.6 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main arm64 libsemanage-common all 2.9-3build1 [9736 B] Get:11 http://ftpmaster.internal/ubuntu focal/main arm64 libsemanage1 arm64 2.9-3build1 [79.3 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 lsb-base all 11.1.0ubuntu1 [12.2 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libapparmor1 arm64 2.13.3-5ubuntu2 [33.5 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main arm64 libcryptsetup12 arm64 2:2.2.1-1ubuntu1 [165 kB] Get:15 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 binutils-aarch64-linux-gnu arm64 2.33.1-1ubuntu1 [2021 kB] Get:16 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libbinutils arm64 2.33.1-1ubuntu1 [470 kB] Get:17 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 binutils arm64 2.33.1-1ubuntu1 [3376 B] Get:18 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 binutils-common arm64 2.33.1-1ubuntu1 [203 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 11.6 MB in 7s (1731 kB/s) (Reading database ... 12731 files and directories currently installed.) Preparing to unpack .../base-files_11ubuntu1_arm64.deb ... Unpacking base-files (11ubuntu1) over (10.2ubuntu7) ... Setting up base-files (11ubuntu1) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Updating /root/.profile to current default. (Reading database ... 12731 files and directories currently installed.) Preparing to unpack .../perl_5.30.0-7_arm64.deb ... Unpacking perl (5.30.0-7) over (5.28.1-6build1) ... Replacing files in old package perl-base (5.28.1-6build1) ... Selecting previously unselected package perl-modules-5.30. Preparing to unpack .../perl-modules-5.30_5.30.0-7_all.deb ... Unpacking perl-modules-5.30 (5.30.0-7) ... Selecting previously unselected package libperl5.30:arm64. Preparing to unpack .../libperl5.30_5.30.0-7_arm64.deb ... Unpacking libperl5.30:arm64 (5.30.0-7) ... Preparing to unpack .../perl-base_5.30.0-7_arm64.deb ... Unpacking perl-base (5.30.0-7) over (5.28.1-6build1) ... Setting up perl-base (5.30.0-7) ... (Reading database ... 14641 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a2.8.5-2ubuntu2_all.deb ... Unpacking libaudit-common (1:2.8.5-2ubuntu2) over (1:2.8.5-2ubuntu1) ... Setting up libaudit-common (1:2.8.5-2ubuntu2) ... (Reading database ... 14641 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a2.8.5-2ubuntu2_arm64.deb ... Unpacking libaudit1:arm64 (1:2.8.5-2ubuntu2) over (1:2.8.5-2ubuntu1) ... Setting up libaudit1:arm64 (1:2.8.5-2ubuntu2) ... (Reading database ... 14641 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.8.5-3ubuntu1_arm64.deb ... Unpacking libgcrypt20:arm64 (1.8.5-3ubuntu1) over (1.8.4-5ubuntu2) ... Setting up libgcrypt20:arm64 (1.8.5-3ubuntu1) ... (Reading database ... 14641 files and directories currently installed.) Preparing to unpack .../libselinux1_2.9-2build1_arm64.deb ... Unpacking libselinux1:arm64 (2.9-2build1) over (2.9-2) ... Setting up libselinux1:arm64 (2.9-2build1) ... (Reading database ... 14641 files and directories currently installed.) Preparing to unpack .../libsemanage-common_2.9-3build1_all.deb ... Unpacking libsemanage-common (2.9-3build1) over (2.9-3) ... Setting up libsemanage-common (2.9-3build1) ... (Reading database ... 14641 files and directories currently installed.) Preparing to unpack .../libsemanage1_2.9-3build1_arm64.deb ... Unpacking libsemanage1:arm64 (2.9-3build1) over (2.9-3) ... Setting up libsemanage1:arm64 (2.9-3build1) ... (Reading database ... 14641 files and directories currently installed.) Preparing to unpack .../0-lsb-base_11.1.0ubuntu1_all.deb ... Unpacking lsb-base (11.1.0ubuntu1) over (11.0.1ubuntu1) ... Preparing to unpack .../1-libapparmor1_2.13.3-5ubuntu2_arm64.deb ... Unpacking libapparmor1:arm64 (2.13.3-5ubuntu2) over (2.13.3-5ubuntu1) ... Preparing to unpack .../2-libcryptsetup12_2%3a2.2.1-1ubuntu1_arm64.deb ... Unpacking libcryptsetup12:arm64 (2:2.2.1-1ubuntu1) over (2:2.2.0-3ubuntu1) ... Preparing to unpack .../3-binutils-aarch64-linux-gnu_2.33.1-1ubuntu1_arm64.deb ... Unpacking binutils-aarch64-linux-gnu (2.33.1-1ubuntu1) over (2.33-2ubuntu1) ... Preparing to unpack .../4-libbinutils_2.33.1-1ubuntu1_arm64.deb ... Unpacking libbinutils:arm64 (2.33.1-1ubuntu1) over (2.33-2ubuntu1) ... Preparing to unpack .../5-binutils_2.33.1-1ubuntu1_arm64.deb ... Unpacking binutils (2.33.1-1ubuntu1) over (2.33-2ubuntu1) ... Preparing to unpack .../6-binutils-common_2.33.1-1ubuntu1_arm64.deb ... Unpacking binutils-common:arm64 (2.33.1-1ubuntu1) over (2.33-2ubuntu1) ... Setting up lsb-base (11.1.0ubuntu1) ... Setting up libapparmor1:arm64 (2.13.3-5ubuntu2) ... Setting up perl-modules-5.30 (5.30.0-7) ... Setting up binutils-common:arm64 (2.33.1-1ubuntu1) ... Setting up libperl5.30:arm64 (5.30.0-7) ... Setting up libcryptsetup12:arm64 (2:2.2.1-1ubuntu1) ... Setting up libbinutils:arm64 (2.33.1-1ubuntu1) ... Setting up binutils-aarch64-linux-gnu (2.33.1-1ubuntu1) ... Setting up binutils (2.33.1-1ubuntu1) ... Setting up perl (5.30.0-7) ... Processing triggers for libc-bin (2.30-0ubuntu2) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-17940056 arm64 focal-proposed -c chroot:build-PACKAGEBUILD-17940056 --arch=arm64 --dist=focal-proposed --nolog python-pysam_0.15.2+ds-2build1.dsc Initiating build PACKAGEBUILD-17940056 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-165-generic #193-Ubuntu SMP Tue Sep 17 17:45:45 UTC 2019 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-065.buildd +==============================================================================+ | python-pysam 0.15.2+ds-2build1 (arm64) 20 Oct 2019 21:33 | +==============================================================================+ Package: python-pysam Version: 0.15.2+ds-2build1 Source Version: 0.15.2+ds-2build1 Distribution: focal-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/python-pysam-Ur4sdb/python-pysam-0.15.2+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-Ur4sdb' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-17940056/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.15.2+ds-2build1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-kJHZmk/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-kJHZmk/apt_archive ./ InRelease Get:2 copy:/<>/resolver-kJHZmk/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-kJHZmk/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-kJHZmk/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-kJHZmk/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (85.5 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-kJHZmk/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14640 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest Filtered Build-Depends: debhelper (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<>/resolver-c2iice/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'. Ign:1 copy:/<>/resolver-c2iice/apt_archive ./ InRelease Get:2 copy:/<>/resolver-c2iice/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-c2iice/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-c2iice/apt_archive ./ Sources [315 B] Get:5 copy:/<>/resolver-c2iice/apt_archive ./ Packages [621 B] Fetched 3055 B in 0s (147 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install python-pysam build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-atomicwrites python-attr python-configparser python-contextlib2 python-dev python-funcsigs python-importlib-metadata python-minimal python-more-itertools python-packaging python-pathlib2 python-pkg-resources python-pluggy python-py python-pyparsing python-pytest python-scandir python-setuptools python-six python-wcwidth python-zipp python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-atomicwrites python3-attr python3-dev python3-distutils python3-importlib-metadata python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pyparsing python3-pytest python3-setuptools python3-six python3-wcwidth python3-zipp python3.7 python3.7-dev python3.7-minimal python3.8 python3.8-dev python3.8-minimal samtools tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc python-numpy python-matplotlib texlive-latex-recommended wamerican | wordlist whois vacation cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk python-attr-doc python-funcsigs-doc subversion python-pytest-xdist python-pyparsing-doc python-mock python-setuptools-doc python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.7-venv python3.7-doc python3.8-venv python3.8-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-atomicwrites python-attr python-configparser python-contextlib2 python-dev python-funcsigs python-importlib-metadata python-minimal python-more-itertools python-packaging python-pathlib2 python-pkg-resources python-pluggy python-py python-pyparsing python-pytest python-scandir python-setuptools python-six python-wcwidth python-zipp python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-atomicwrites python3-attr python3-dev python3-distutils python3-importlib-metadata python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pyparsing python3-pytest python3-setuptools python3-six python3-wcwidth python3-zipp python3.7 python3.7-dev python3.7-minimal python3.8 python3.8-dev python3.8-minimal samtools sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev 0 upgraded, 153 newly installed, 0 to remove and 0 not upgraded. Need to get 57.6 MB of archives. After this operation, 235 MB of additional disk space will be used. Get:1 copy:/<>/resolver-c2iice/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [952 B] Get:2 http://ftpmaster.internal/ubuntu focal/main arm64 libpython3.7-minimal arm64 3.7.5-1ubuntu1 [544 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main arm64 libexpat1 arm64 2.2.7-2 [61.2 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main arm64 python3.7-minimal arm64 3.7.5-1ubuntu1 [1719 kB] Get:5 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3-minimal arm64 3.7.5-1ubuntu1 [23.3 kB] Get:6 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 mime-support all 3.64ubuntu1 [30.6 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main arm64 libmpdec2 arm64 2.4.2-2 [74.0 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main arm64 libpython3.7-stdlib arm64 3.7.5-1ubuntu1 [1712 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main arm64 python3.7 arm64 3.7.5-1ubuntu1 [301 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libpython3-stdlib arm64 3.7.5-1ubuntu1 [6844 B] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3 arm64 3.7.5-1ubuntu1 [47.2 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main arm64 libbsd0 arm64 0.10.0-1 [43.7 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main arm64 bsdmainutils arm64 11.1.2ubuntu2 [175 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main arm64 groff-base arm64 1.22.4-3 [813 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main arm64 libpipeline1 arm64 1.5.1-2 [24.4 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main arm64 man-db arm64 2.8.7-3 [1096 kB] Get:18 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 libpython2.7-minimal arm64 2.7.17-1 [335 kB] Get:19 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 python2.7-minimal arm64 2.7.17-1 [1226 kB] Get:20 http://ftpmaster.internal/ubuntu focal/universe arm64 python2-minimal arm64 2.7.17-1 [27.8 kB] Get:21 http://ftpmaster.internal/ubuntu focal/universe arm64 python-minimal arm64 2.7.17-1 [5996 B] Get:22 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 libpython2.7-stdlib arm64 2.7.17-1 [1866 kB] Get:23 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 python2.7 arm64 2.7.17-1 [248 kB] Get:24 http://ftpmaster.internal/ubuntu focal/universe arm64 libpython2-stdlib arm64 2.7.17-1 [7400 B] Get:25 http://ftpmaster.internal/ubuntu focal/universe arm64 libpython-stdlib arm64 2.7.17-1 [5836 B] Get:26 http://ftpmaster.internal/ubuntu focal/universe arm64 python2 arm64 2.7.17-1 [26.5 kB] Get:27 http://ftpmaster.internal/ubuntu focal/universe arm64 python arm64 2.7.17-1 [7836 B] Get:28 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libpython3.8-minimal arm64 3.8.0-2 [701 kB] Get:29 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3.8-minimal arm64 3.8.0-2 [1818 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main arm64 libmagic-mgc arm64 1:5.37-5 [209 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main arm64 libmagic1 arm64 1:5.37-5 [70.9 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main arm64 file arm64 1:5.37-5 [23.2 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main arm64 libelf1 arm64 0.176-1.1 [43.6 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main arm64 libglib2.0-0 arm64 2.62.1-1 [1178 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main arm64 libicu63 arm64 63.2-2 [8146 kB] Get:36 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libxml2 arm64 2.9.4+dfsg1-7ubuntu4 [576 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main arm64 python3-pkg-resources all 41.1.0-1 [100 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main arm64 python3-six all 1.12.0-2build1 [11.7 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main arm64 gettext-base arm64 0.19.8.1-9 [48.0 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main arm64 libkrb5support0 arm64 1.17-6 [30.8 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main arm64 libk5crypto3 arm64 1.17-6 [80.5 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main arm64 libkeyutils1 arm64 1.6-6ubuntu1 [10.1 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main arm64 libkrb5-3 arm64 1.17-6 [312 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main arm64 libgssapi-krb5-2 arm64 1.17-6 [113 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main arm64 libpsl5 arm64 0.20.2-2 [49.9 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main arm64 libsigsegv2 arm64 2.12-2 [13.3 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main arm64 m4 arm64 1.4.18-2 [194 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main arm64 autoconf all 2.69-11ubuntu1 [321 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main arm64 autotools-dev all 20180224.1 [39.6 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main arm64 automake all 1:1.16.1-4ubuntu3 [522 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main arm64 autopoint all 0.19.8.1-9 [412 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main arm64 libroken18-heimdal arm64 7.5.0+dfsg-3build1 [39.4 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main arm64 libasn1-8-heimdal arm64 7.5.0+dfsg-3build1 [150 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main arm64 libheimbase1-heimdal arm64 7.5.0+dfsg-3build1 [27.9 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main arm64 libhcrypto4-heimdal arm64 7.5.0+dfsg-3build1 [85.9 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main arm64 libwind0-heimdal arm64 7.5.0+dfsg-3build1 [47.2 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main arm64 libhx509-5-heimdal arm64 7.5.0+dfsg-3build1 [98.7 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main arm64 libkrb5-26-heimdal arm64 7.5.0+dfsg-3build1 [191 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main arm64 libheimntlm0-heimdal arm64 7.5.0+dfsg-3build1 [14.7 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main arm64 libgssapi3-heimdal arm64 7.5.0+dfsg-3build1 [88.0 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-1build3 [14.8 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main arm64 libsasl2-2 arm64 2.1.27+dfsg-1build3 [48.5 kB] Get:63 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libldap-common all 2.4.48+dfsg-1ubuntu2 [17.3 kB] Get:64 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libldap-2.4-2 arm64 2.4.48+dfsg-1ubuntu2 [146 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main arm64 libnghttp2-14 arm64 1.39.2-1 [75.4 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2 [49.8 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main arm64 libssh-4 arm64 0.9.0-1ubuntu1 [185 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main arm64 libcurl3-gnutls arm64 7.65.3-1ubuntu3 [209 kB] Get:69 http://ftpmaster.internal/ubuntu focal/universe arm64 libdeflate0 arm64 1.2-1 [51.4 kB] Get:70 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 libhts2 arm64 1.9-11 [264 kB] Get:71 http://ftpmaster.internal/ubuntu focal/universe arm64 bcftools arm64 1.9-1 [477 kB] Get:72 http://ftpmaster.internal/ubuntu focal/universe arm64 cython arm64 0.29.13-0ubuntu2 [1260 kB] Get:73 http://ftpmaster.internal/ubuntu focal/universe arm64 cython3 arm64 0.29.13-0ubuntu2 [1771 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main arm64 libtool all 2.4.6-11 [194 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main arm64 dh-autoreconf all 19 [16.1 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main arm64 libarchive-zip-perl all 1.65-1 [83.6 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:78 http://ftpmaster.internal/ubuntu focal/main arm64 libfile-stripnondeterminism-perl all 1.6.0-1 [16.2 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main arm64 dh-strip-nondeterminism all 1.6.0-1 [5208 B] Get:80 http://ftpmaster.internal/ubuntu focal/main arm64 dwz arm64 0.13-1 [73.4 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main arm64 libdebhelper-perl all 12.6.1ubuntu2 [52.2 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main arm64 libcroco3 arm64 0.6.13-1 [77.1 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main arm64 gettext arm64 0.19.8.1-9 [853 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main arm64 po-debconf all 1.0.21 [233 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main arm64 debhelper all 12.6.1ubuntu2 [872 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main arm64 python3-lib2to3 all 3.7.5-1build1 [75.6 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main arm64 python3-distutils all 3.7.5-1build1 [142 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main arm64 dh-python all 4.20191017ubuntu1 [88.5 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main arm64 libexpat1-dev arm64 2.2.7-2 [103 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main arm64 liblzma-dev arm64 5.2.4-1 [144 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1ubuntu3 [170 kB] Get:93 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 libhts-dev arm64 1.9-11 [4325 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main arm64 libjs-jquery all 3.3.1~dfsg-3 [329 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main arm64 libjs-underscore all 1.9.1~dfsg-1 [98.6 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main arm64 libjs-sphinxdoc all 1.8.5-3 [96.5 kB] Get:97 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 libpython2.7 arm64 2.7.17-1 [957 kB] Get:98 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 libpython2.7-dev arm64 2.7.17-1 [2350 kB] Get:99 http://ftpmaster.internal/ubuntu focal/universe arm64 libpython2-dev arm64 2.7.17-1 [7460 B] Get:100 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focal/universe arm64 python-all arm64 2.7.17-1 [1088 B] Get:110 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 python2.7-dev arm64 2.7.17-1 [280 kB] Get:111 http://ftpmaster.internal/ubuntu focal/universe arm64 python2-dev arm64 2.7.17-1 [1268 B] Get:112 http://ftpmaster.internal/ubuntu focal/universe arm64 python-dev arm64 2.7.17-1 [1236 B] Get:113 http://ftpmaster.internal/ubuntu focal/universe arm64 python-all-dev arm64 2.7.17-1 [1112 B] Get:114 http://ftpmaster.internal/ubuntu focal/universe arm64 python-atomicwrites all 1.1.5-2 [6856 B] Get:115 http://ftpmaster.internal/ubuntu focal/universe arm64 python-attr all 18.2.0-1 [29.6 kB] Get:116 http://ftpmaster.internal/ubuntu focal/universe arm64 python-configparser all 3.5.0b2-3 [62.7 kB] Get:117 http://ftpmaster.internal/ubuntu focal/universe arm64 python-contextlib2 all 0.5.5-3 [10.7 kB] Get:118 http://ftpmaster.internal/ubuntu focal/universe arm64 python-funcsigs all 1.0.2-4 [13.5 kB] Get:119 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python-pluggy all 0.13.0-0ubuntu1 [18.2 kB] Get:129 http://ftpmaster.internal/ubuntu focal/universe arm64 python-py all 1.8.0-1 [65.2 kB] Get:130 http://ftpmaster.internal/ubuntu focal/universe arm64 python-wcwidth all 0.1.7+dfsg1-6 [15.3 kB] Get:131 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 python-pytest all 4.6.5-2 [177 kB] Get:132 http://ftpmaster.internal/ubuntu focal/universe arm64 python-setuptools all 41.1.0-1 [330 kB] Get:133 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3.8 arm64 3.8.0-2 [355 kB] Get:134 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3-all arm64 3.7.5-1ubuntu1 [1120 B] Get:135 http://ftpmaster.internal/ubuntu focal/main arm64 python3.7-dev arm64 3.7.5-1ubuntu1 [515 kB] Get:136 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3-dev arm64 3.7.5-1ubuntu1 [1312 B] Get:137 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3.8-dev arm64 3.8.0-2 [511 kB] Get:138 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3-all-dev arm64 3.7.5-1ubuntu1 [1128 B] Get:139 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-atomicwrites all 1.1.5-2 [6932 B] Get:140 http://ftpmaster.internal/ubuntu focal/main arm64 python3-attr all 18.2.0-1 [29.6 kB] Get:141 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-zipp all 0.5.2-2 [4900 B] Get:142 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-importlib-metadata all 0.23-0ubuntu1 [9396 B] Get:143 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-more-itertools all 4.2.0-1 [39.3 kB] Get:144 http://ftpmaster.internal/ubuntu focal/main arm64 python3-pyparsing all 2.2.0+dfsg1-2 [52.2 kB] Get:145 http://ftpmaster.internal/ubuntu focal/main arm64 python3-packaging all 19.1-2 [21.7 kB] Get:146 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 python3-pluggy all 0.13.0-0ubuntu1 [18.3 kB] Get:147 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-py all 1.8.0-1 [65.3 kB] Get:148 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-wcwidth all 0.1.7+dfsg1-6 [15.4 kB] Get:149 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 python3-pytest all 4.6.5-2 [177 kB] Get:150 http://ftpmaster.internal/ubuntu focal/main arm64 python3-setuptools all 41.1.0-1 [253 kB] Get:151 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 samtools arm64 1.9-5 [404 kB] Get:152 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 tabix arm64 1.9-11 [260 kB] Get:153 http://ftpmaster.internal/ubuntu focal/main arm64 dh-exec arm64 0.23.2 [24.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 57.6 MB in 29s (2000 kB/s) Selecting previously unselected package libpython3.7-minimal:arm64. (Reading database ... 14640 files and directories currently installed.) Preparing to unpack .../libpython3.7-minimal_3.7.5-1ubuntu1_arm64.deb ... Unpacking libpython3.7-minimal:arm64 (3.7.5-1ubuntu1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.2.7-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.7-2) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../python3.7-minimal_3.7.5-1ubuntu1_arm64.deb ... Unpacking python3.7-minimal (3.7.5-1ubuntu1) ... Setting up libpython3.7-minimal:arm64 (3.7.5-1ubuntu1) ... Setting up libexpat1:arm64 (2.2.7-2) ... Setting up python3.7-minimal (3.7.5-1ubuntu1) ... Selecting previously unselected package python3-minimal. (Reading database ... 14889 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.5-1ubuntu1_arm64.deb ... Unpacking python3-minimal (3.7.5-1ubuntu1) ... Selecting previously unselected package mime-support. 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Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.5-1ubuntu1) ... Setting up cython (0.29.13-0ubuntu2) ... Setting up gettext (0.19.8.1-9) ... Setting up libpython3-dev:arm64 (3.7.5-1ubuntu1) ... Setting up python2-dev (2.7.17-1) ... Setting up python-pkg-resources (41.1.0-1) ... Setting up libhx509-5-heimdal:arm64 (7.5.0+dfsg-3build1) ... Setting up python-zipp (0.5.2-2) ... Setting up python3 (3.7.5-1ubuntu1) ... Setting up python-all (2.7.17-1) ... Setting up python3-zipp (0.5.2-2) ... Setting up python-attr (18.2.0-1) ... Setting up man-db (2.8.7-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3.7-dev (3.7.5-1ubuntu1) ... Setting up python-atomicwrites (1.1.5-2) ... Setting up python3-atomicwrites (1.1.5-2) ... 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Processing triggers for libc-bin (2.30-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-165-generic arm64 (aarch64) Toolchain package versions: binutils_2.33.1-1ubuntu1 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-9ubuntu2 gcc-9_9.2.1-9ubuntu2 libc6-dev_2.30-0ubuntu2 libstdc++-9-dev_9.2.1-9ubuntu2 libstdc++6_9.2.1-9ubuntu2 linux-libc-dev_5.3.0-18.19 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.4 autoconf_2.69-11ubuntu1 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11ubuntu1 base-passwd_3.5.46 bash_5.0-4ubuntu1 bcftools_1.9-1 binutils_2.33.1-1ubuntu1 binutils-aarch64-linux-gnu_2.33.1-1ubuntu1 binutils-common_2.33.1-1ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu2 build-essential_12.8ubuntu1 bzip2_1.0.6-9.2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 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python-pytest_4.6.5-2 python-scandir_1.10.0-2 python-setuptools_41.1.0-1 python-six_1.12.0-2build1 python-wcwidth_0.1.7+dfsg1-6 python-zipp_0.5.2-2 python2_2.7.17-1 python2-dev_2.7.17-1 python2-minimal_2.7.17-1 python2.7_2.7.17-1 python2.7-dev_2.7.17-1 python2.7-minimal_2.7.17-1 python3_3.7.5-1ubuntu1 python3-all_3.7.5-1ubuntu1 python3-all-dev_3.7.5-1ubuntu1 python3-atomicwrites_1.1.5-2 python3-attr_18.2.0-1 python3-dev_3.7.5-1ubuntu1 python3-distutils_3.7.5-1build1 python3-importlib-metadata_0.23-0ubuntu1 python3-lib2to3_3.7.5-1build1 python3-minimal_3.7.5-1ubuntu1 python3-more-itertools_4.2.0-1 python3-packaging_19.1-2 python3-pkg-resources_41.1.0-1 python3-pluggy_0.13.0-0ubuntu1 python3-py_1.8.0-1 python3-pyparsing_2.2.0+dfsg1-2 python3-pytest_4.6.5-2 python3-setuptools_41.1.0-1 python3-six_1.12.0-2build1 python3-wcwidth_0.1.7+dfsg1-6 python3-zipp_0.5.2-2 python3.7_3.7.5-1ubuntu1 python3.7-dev_3.7.5-1ubuntu1 python3.7-minimal_3.7.5-1ubuntu1 python3.8_3.8.0-2 python3.8-dev_3.8.0-2 python3.8-minimal_3.8.0-2 readline-common_8.0-3 samtools_1.9-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_242-7ubuntu3 systemd-sysv_242-7ubuntu3 sysvinit-utils_2.95-5ubuntu2 tabix_1.9-11 tar_1.30+dfsg-6 tzdata_2019c-3 ubuntu-keyring_2018.09.18.1 util-linux_2.34-0.1ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Oct 18 18:51:35 2019 UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pysam_0.15.2+ds-2build1.dsc dpkg-source: info: extracting python-pysam in python-pysam-0.15.2+ds dpkg-source: info: unpacking python-pysam_0.15.2+ds.orig.tar.xz dpkg-source: info: unpacking python-pysam_0.15.2+ds-2build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_remote.patch dpkg-source: info: applying skip_test_needing_missing_data.patch dpkg-source: info: applying spelling dpkg-source: info: applying test_index_not_compression Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-17940056 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-17940056 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-17940056 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.15.2+ds-2build1 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.15.2+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ with_md.sam.gz \ *.fq.gz make[1]: Leaving directory '/<>/python-pysam-0.15.2+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.15.2+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/<>/python-pysam-0.15.2+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete #find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully find . -name "*.bai*" -delete find . -name "*.cram*" -delete #find . -name "*.bam" -delete # which deletes files tested rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh clean --with python2,python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/python-pysam-0.15.2+ds' dh_auto_clean I: pybuild base:217: python2.7 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:217: python3.8 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.8' does not exist -- can't clean it I: pybuild base:217: python3.7 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info make[1]: Leaving directory '/<>/python-pysam-0.15.2+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with python2,python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config I: pybuild base:217: python3.8 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config I: pybuild base:217: python3.7 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python2 setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/version.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/config.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libcbcf.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcsamtools.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/cbcftools_util.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libchtslib.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libchtslib' extension creating build creating build/temp.linux-arm64-2.7 creating build/temp.linux-arm64-2.7/pysam aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-arm64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-arm64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libchtslib.o build/temp.linux-arm64-2.7/pysam/htslib_util.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libcsamtools.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcsamtools' extension creating build/temp.linux-arm64-2.7/samtools creating build/temp.linux-arm64-2.7/samtools/lz4 aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-arm64-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/samtools.pysam.c -o build/temp.linux-arm64-2.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/stdio.h:867, from samtools/samtools.pysam.h:4, from samtools/sam_opts.c.pysam.c:1: In function ‘fprintf’, inlined from ‘parse_sam_global_opt’ at samtools/sam_opts.c.pysam.c:87:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:100:10: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 100 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/lz4/lz4.c -o build/temp.linux-arm64-2.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libcsamtools.o build/temp.linux-arm64-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_markdup.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-arm64-2.7/samtools/samtools.pysam.o build/temp.linux-arm64-2.7/samtools/sam_view.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_import.c.pysam.o build/temp.linux-arm64-2.7/samtools/cut_target.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-arm64-2.7/samtools/tmp_file.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_split.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_index.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_md.c.pysam.o build/temp.linux-arm64-2.7/samtools/sample.c.pysam.o build/temp.linux-arm64-2.7/samtools/dict.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-arm64-2.7/samtools/bamtk.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-arm64-2.7/samtools/bedidx.c.pysam.o build/temp.linux-arm64-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-arm64-2.7/samtools/padding.c.pysam.o build/temp.linux-arm64-2.7/samtools/phase.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-arm64-2.7/samtools/faidx.c.pysam.o build/temp.linux-arm64-2.7/samtools/stats.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam_header.c.pysam.o build/temp.linux-arm64-2.7/samtools/bedcov.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-arm64-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_color.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-arm64-2.7/samtools/lz4/lz4.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libcbcftools.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcbcftools' extension creating build/temp.linux-arm64-2.7/bcftools aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-arm64-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/reheader.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In function ‘realign’, inlined from ‘normalize_line’ at bcftools/vcfnorm.c.pysam.c:1719:23: bcftools/vcfnorm.c.pysam.c:347:17: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 347 | error("Non-ACGTN alternate allele at %s:%d .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bcftools.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In function ‘init_data’, inlined from ‘main_vcfcall’ at bcftools/vcfcall.c.pysam.c:810:5: bcftools/vcfcall.c.pysam.c:423:39: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 423 | args->aux.ploidy = (uint8_t*) malloc(args->nsamples); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:29, from /usr/include/htslib/vcf.h:40, from bcftools/vcfcall.c.pysam.c:34: bcftools/vcfcall.c.pysam.c: In function ‘main_vcfcall’: /usr/include/stdlib.h:539:14: note: in a call to allocation function ‘malloc’ declared here 539 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:684:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 684 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:29, from /usr/include/htslib/vcf.h:40, from bcftools/vcfmerge.c.pysam.c:33: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ bcftools/vcfmerge.c.pysam.c: In function ‘merge_vcf’: bcftools/vcfmerge.c.pysam.c:2336:46: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 2336 | char buf[10]; snprintf(buf,10,"%d",i+1); | ^ In file included from /usr/include/stdio.h:867, from bcftools/bcftools.pysam.h:4, from bcftools/vcfmerge.c.pysam.c:1: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 10 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libcbcftools.o build/temp.linux-arm64-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfsort.c.pysam.o build/temp.linux-arm64-2.7/bcftools/reheader.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bin.c.pysam.o build/temp.linux-arm64-2.7/bcftools/em.c.pysam.o build/temp.linux-arm64-2.7/bcftools/main.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-arm64-2.7/bcftools/regidx.c.pysam.o build/temp.linux-arm64-2.7/bcftools/kmin.c.pysam.o build/temp.linux-arm64-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-arm64-2.7/bcftools/consensus.c.pysam.o build/temp.linux-arm64-2.7/bcftools/filter.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bcftools.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-arm64-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/prob1.c.pysam.o build/temp.linux-arm64-2.7/bcftools/ccall.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-arm64-2.7/bcftools/hclust.c.pysam.o build/temp.linux-arm64-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-arm64-2.7/bcftools/mcall.c.pysam.o build/temp.linux-arm64-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-arm64-2.7/bcftools/convert.c.pysam.o build/temp.linux-arm64-2.7/bcftools/HMM.c.pysam.o build/temp.linux-arm64-2.7/bcftools/tabix.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-arm64-2.7/bcftools/csq.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-arm64-2.7/bcftools/version.c.pysam.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN cythoning pysam/libcutils.pyx to pysam/libcutils.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libcutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcutils' extension aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-arm64-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6101:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration] 6101 | bcftools_set_stderr(__pyx_t_9); | ^~~~~~~~~~~~~~~~~~~ | samtools_set_stderr pysam/libcutils.c:6245:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration] 6245 | bcftools_set_stdout_fn(__pyx_t_12); | ^~~~~~~~~~~~~~~~~~~~~~ | samtools_set_stdout_fn pysam/libcutils.c:6256:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration] 6256 | bcftools_set_stdout(__pyx_t_9); | ^~~~~~~~~~~~~~~~~~~ | samtools_set_stdout pysam/libcutils.c:7011:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration] 7011 | bcftools_set_optind(1); | ^~~~~~~~~~~~~~~~~~~ | samtools_set_optind pysam/libcutils.c:7090:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration] 7090 | __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); | ^~~~~~~~~~~~~ | samtools_main pysam/libcutils.c:7159:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration] 7159 | bcftools_unset_stderr(); | ^~~~~~~~~~~~~~~~~~~~~ | samtools_unset_stderr pysam/libcutils.c:7195:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration] 7195 | bcftools_unset_stdout(); | ^~~~~~~~~~~~~~~~~~~~~ | samtools_unset_stdout aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-arm64-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libcutils.o build/temp.linux-arm64-2.7/pysam/pysam_util.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -Wl,-rpath,$ORIGIN cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libcalignmentfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcalignmentfile.pyx:2527:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2532:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2537:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation building 'pysam.libcalignmentfile' extension aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-arm64-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:29343:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] 29343 | __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); | ~^~~~~~~~~~~~~~~~~~~ | | | bam_pileup1_t ** {aka struct **} In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:604: /usr/include/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct **’} 686 | int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); | ~~~~~~~~~~~~~~~~~~~~~~^~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:27596:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] 27596 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:13699:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] 13699 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libcalignmentfile.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libcsamfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcsamfile' extension aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-arm64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libcsamfile.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libcalignedsegment.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcalignedsegment' extension aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-arm64-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: pysam/libcalignedsegment.c:14237:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result] 14237 | (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libcalignedsegment.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN cythoning pysam/libctabix.pyx to pysam/libctabix.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libctabix.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libctabix' extension aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-arm64-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:8643:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 8643 | __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); | ^ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’: pysam/libctabix.c:13709:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 13709 | __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error) | ^~~~~~~~ pysam/libctabix.c:13741:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 13741 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error) | ^~~~~~~~ pysam/libctabix.c:14111:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 14111 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) | ^~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libctabix.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -Wl,-rpath,$ORIGIN cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libcfaidx.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcfaidx' extension aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-arm64-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libcfaidx.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbcf.pyx to pysam/libcbcf.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libcbcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcbcf' extension aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-arm64-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:32825:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] 32825 | __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen)); | ^~~~~~~~~~~~ In file included from pysam/htslib_util.h:5, from pysam/libcbcf.c:603: /usr/include/htslib/vcf.h:439:11: note: declared here 439 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libcbcf.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libcbgzf.pyx tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcbgzf' extension aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-arm64-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libcbgzf.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libctabixproxies.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libctabixproxies' extension aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-arm64-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libctabixproxies.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN cythoning pysam/libcvcf.pyx to pysam/libcvcf.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/pysam/libcvcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libcvcf' extension aarch64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-arm64-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QeAaaM/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-arm64-2.7/pysam/libcvcf.o -L/<>/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -Wl,-rpath,$ORIGIN I: pybuild base:217: /usr/bin/python3.8 setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/version.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/config.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libcbcf.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcsamtools.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/cbcftools_util.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/win32 Fixing /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/samtools.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/Pileup.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/version.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/bcftools.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/utils.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/samtools.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/Pileup.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/version.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/bcftools.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/utils.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.linux-arm64-3.8 creating build/temp.linux-arm64-3.8/pysam aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libchtslib.c -o build/temp.linux-arm64-3.8/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/htslib_util.c -o build/temp.linux-arm64-3.8/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libchtslib.o build/temp.linux-arm64-3.8/pysam/htslib_util.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libchtslib.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) building 'pysam.libcsamtools' extension creating build/temp.linux-arm64-3.8/samtools creating build/temp.linux-arm64-3.8/samtools/lz4 aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libcsamtools.c -o build/temp.linux-arm64-3.8/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/string.h:494, from samtools/bam_sort.c.pysam.c:36: In function ‘strncpy’, inlined from ‘bam_sort_core_ext’ at samtools/bam_sort.c.pysam.c:2144:9: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 2 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/samtools.pysam.c -o build/temp.linux-arm64-3.8/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/sam_view.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_import.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/cut_target.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_split.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_index.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_md.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/sample.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/dict.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bamtk.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bedidx.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/padding.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/phase.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/faidx.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/stats.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/sam_header.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bedcov.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/sam.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_color.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-arm64-3.8/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/stdio.h:867, from samtools/samtools.pysam.h:4, from samtools/sam_opts.c.pysam.c:1: In function ‘fprintf’, inlined from ‘parse_sam_global_opt’ at samtools/sam_opts.c.pysam.c:87:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:100:10: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 100 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c samtools/lz4/lz4.c -o build/temp.linux-arm64-3.8/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libcsamtools.o build/temp.linux-arm64-3.8/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_markdup.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_lpileup.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_plbuf.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_sort.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_quickcheck.c.pysam.o build/temp.linux-arm64-3.8/samtools/samtools.pysam.o build/temp.linux-arm64-3.8/samtools/sam_view.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_mate.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_rmdupse.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_import.c.pysam.o build/temp.linux-arm64-3.8/samtools/cut_target.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_aux.c.pysam.o build/temp.linux-arm64-3.8/samtools/tmp_file.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_stat.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_split.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_index.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_md.c.pysam.o build/temp.linux-arm64-3.8/samtools/sample.c.pysam.o build/temp.linux-arm64-3.8/samtools/dict.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam2bcf.c.pysam.o build/temp.linux-arm64-3.8/samtools/bamtk.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_reheader.c.pysam.o build/temp.linux-arm64-3.8/samtools/bedidx.c.pysam.o build/temp.linux-arm64-3.8/samtools/stats_isize.c.pysam.o build/temp.linux-arm64-3.8/samtools/padding.c.pysam.o build/temp.linux-arm64-3.8/samtools/phase.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam2depth.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_plcmd.c.pysam.o build/temp.linux-arm64-3.8/samtools/faidx.c.pysam.o build/temp.linux-arm64-3.8/samtools/stats.c.pysam.o build/temp.linux-arm64-3.8/samtools/sam_header.c.pysam.o build/temp.linux-arm64-3.8/samtools/bedcov.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_cat.c.pysam.o build/temp.linux-arm64-3.8/samtools/sam.c.pysam.o build/temp.linux-arm64-3.8/samtools/sam_utils.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_rmdup.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_addrprg.c.pysam.o build/temp.linux-arm64-3.8/samtools/bamshuf.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_color.c.pysam.o build/temp.linux-arm64-3.8/samtools/bam_flags.c.pysam.o build/temp.linux-arm64-3.8/samtools/sam_opts.c.pysam.o build/temp.linux-arm64-3.8/samtools/lz4/lz4.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamtools.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) building 'pysam.libcbcftools' extension creating build/temp.linux-arm64-3.8/bcftools aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libcbcftools.c -o build/temp.linux-arm64-3.8/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/reheader.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In function ‘realign’, inlined from ‘normalize_line’ at bcftools/vcfnorm.c.pysam.c:1719:23: bcftools/vcfnorm.c.pysam.c:347:17: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 347 | error("Non-ACGTN alternate allele at %s:%d .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/bin.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/em.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/main.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/regidx.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/kmin.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/consensus.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/filter.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/bcftools.pysam.c -o build/temp.linux-arm64-3.8/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/prob1.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/ccall.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/hclust.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/mcall.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/convert.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/HMM.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/tabix.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:684:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 684 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:29, from /usr/include/htslib/vcf.h:40, from bcftools/vcfmerge.c.pysam.c:33: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/csq.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c bcftools/version.c.pysam.c -o build/temp.linux-arm64-3.8/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libcbcftools.o build/temp.linux-arm64-3.8/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-3.8/bcftools/gvcf.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfsom.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfsort.c.pysam.o build/temp.linux-arm64-3.8/bcftools/reheader.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfnorm.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcffilter.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfbuf.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfview.c.pysam.o build/temp.linux-arm64-3.8/bcftools/bam_sample.c.pysam.o build/temp.linux-arm64-3.8/bcftools/bin.c.pysam.o build/temp.linux-arm64-3.8/bcftools/em.c.pysam.o build/temp.linux-arm64-3.8/bcftools/main.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfroh.c.pysam.o build/temp.linux-arm64-3.8/bcftools/regidx.c.pysam.o build/temp.linux-arm64-3.8/bcftools/kmin.c.pysam.o build/temp.linux-arm64-3.8/bcftools/ploidy.c.pysam.o build/temp.linux-arm64-3.8/bcftools/consensus.c.pysam.o build/temp.linux-arm64-3.8/bcftools/filter.c.pysam.o build/temp.linux-arm64-3.8/bcftools/bcftools.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfindex.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfconvert.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfplugin.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfannotate.c.pysam.o build/temp.linux-arm64-3.8/bcftools/tsv2vcf.c.pysam.o build/temp.linux-arm64-3.8/bcftools/bam2bcf.c.pysam.o build/temp.linux-arm64-3.8/bcftools/prob1.c.pysam.o build/temp.linux-arm64-3.8/bcftools/ccall.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcmp.c.pysam.o build/temp.linux-arm64-3.8/bcftools/hclust.c.pysam.o build/temp.linux-arm64-3.8/bcftools/mpileup.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfquery.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfcall.c.pysam.o build/temp.linux-arm64-3.8/bcftools/mcall.c.pysam.o build/temp.linux-arm64-3.8/bcftools/smpl_ilist.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfisec.c.pysam.o build/temp.linux-arm64-3.8/bcftools/convert.c.pysam.o build/temp.linux-arm64-3.8/bcftools/HMM.c.pysam.o build/temp.linux-arm64-3.8/bcftools/tabix.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfcnv.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfmerge.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfstats.c.pysam.o build/temp.linux-arm64-3.8/bcftools/csq.c.pysam.o build/temp.linux-arm64-3.8/bcftools/vcfconcat.c.pysam.o build/temp.linux-arm64-3.8/bcftools/version.c.pysam.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcftools.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcutils.c' Cython extension (up-to-date) building 'pysam.libcutils' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libcutils.c -o build/temp.linux-arm64-3.8/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6101:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration] 6101 | bcftools_set_stderr(__pyx_t_9); | ^~~~~~~~~~~~~~~~~~~ | samtools_set_stderr pysam/libcutils.c:6245:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration] 6245 | bcftools_set_stdout_fn(__pyx_t_12); | ^~~~~~~~~~~~~~~~~~~~~~ | samtools_set_stdout_fn pysam/libcutils.c:6256:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration] 6256 | bcftools_set_stdout(__pyx_t_9); | ^~~~~~~~~~~~~~~~~~~ | samtools_set_stdout pysam/libcutils.c:7011:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration] 7011 | bcftools_set_optind(1); | ^~~~~~~~~~~~~~~~~~~ | samtools_set_optind pysam/libcutils.c:7090:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration] 7090 | __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); | ^~~~~~~~~~~~~ | samtools_main pysam/libcutils.c:7159:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration] 7159 | bcftools_unset_stderr(); | ^~~~~~~~~~~~~~~~~~~~~ | samtools_unset_stderr pysam/libcutils.c:7195:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration] 7195 | bcftools_unset_stdout(); | ^~~~~~~~~~~~~~~~~~~~~ | samtools_unset_stdout pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:511:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] 511 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ pysam/libcutils.c:5833:7: note: ‘__pyx_v_retval’ was declared here 5833 | int __pyx_v_retval; | ^~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/pysam_util.c -o build/temp.linux-arm64-3.8/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libcutils.o build/temp.linux-arm64-3.8/pysam/pysam_util.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-aarch64-linux-gnu -lcsamtools.cpython-38-aarch64-linux-gnu -lcbcftools.cpython-38-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcutils.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) building 'pysam.libcalignmentfile' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libcalignmentfile.c -o build/temp.linux-arm64-3.8/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:29343:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] 29343 | __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); | ~^~~~~~~~~~~~~~~~~~~ | | | bam_pileup1_t ** {aka struct **} In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:604: /usr/include/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct **’} 686 | int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); | ~~~~~~~~~~~~~~~~~~~~~~^~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libcalignmentfile.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-aarch64-linux-gnu -lcutils.cpython-38-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignmentfile.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) building 'pysam.libcsamfile' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libcsamfile.c -o build/temp.linux-arm64-3.8/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libcsamfile.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-aarch64-linux-gnu -lcutils.cpython-38-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamfile.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) building 'pysam.libcalignedsegment' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libcalignedsegment.c -o build/temp.linux-arm64-3.8/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libcalignedsegment.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-aarch64-linux-gnu -lcutils.cpython-38-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignedsegment.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabix.c' Cython extension (up-to-date) building 'pysam.libctabix' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libctabix.c -o build/temp.linux-arm64-3.8/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:8643:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 8643 | __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); | ^ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’: pysam/libctabix.c:13709:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 13709 | __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error) | ^~~~~~~~ pysam/libctabix.c:13741:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 13741 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error) | ^~~~~~~~ pysam/libctabix.c:14111:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 14111 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) | ^~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libctabix.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-aarch64-linux-gnu -lcutils.cpython-38-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabix.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) building 'pysam.libcfaidx' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libcfaidx.c -o build/temp.linux-arm64-3.8/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libcfaidx.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-aarch64-linux-gnu -lcutils.cpython-38-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcfaidx.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbcf.c' Cython extension (up-to-date) building 'pysam.libcbcf' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libcbcf.c -o build/temp.linux-arm64-3.8/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:32825:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] 32825 | __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen)); | ^~~~~~~~~~~~ In file included from pysam/htslib_util.h:5, from pysam/libcbcf.c:603: /usr/include/htslib/vcf.h:439:11: note: declared here 439 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libcbcf.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-aarch64-linux-gnu -lcutils.cpython-38-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcf.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) building 'pysam.libcbgzf' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libcbgzf.c -o build/temp.linux-arm64-3.8/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libcbgzf.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-aarch64-linux-gnu -lcutils.cpython-38-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbgzf.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) building 'pysam.libctabixproxies' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libctabixproxies.c -o build/temp.linux-arm64-3.8/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libctabixproxies.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-aarch64-linux-gnu -lcutils.cpython-38-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabixproxies.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libcvcf' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.8 -c pysam/libcvcf.c -o build/temp.linux-arm64-3.8/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.0’: pysam/libcvcf.c:24840:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] 24840 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/pysam/libcvcf.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-aarch64-linux-gnu -lcutils.cpython-38-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcvcf.cpython-38-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN I: pybuild base:217: /usr/bin/python3 setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/version.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/config.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libcbcf.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcsamtools.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/cbcftools_util.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools creating /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 Fixing /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.linux-arm64-3.7 creating build/temp.linux-arm64-3.7/pysam aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libchtslib.c -o build/temp.linux-arm64-3.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/htslib_util.c -o build/temp.linux-arm64-3.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libchtslib.o build/temp.linux-arm64-3.7/pysam/htslib_util.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) building 'pysam.libcsamtools' extension creating build/temp.linux-arm64-3.7/samtools creating build/temp.linux-arm64-3.7/samtools/lz4 aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcsamtools.c -o build/temp.linux-arm64-3.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/string.h:494, from samtools/bam_sort.c.pysam.c:36: In function ‘strncpy’, inlined from ‘bam_sort_core_ext’ at samtools/bam_sort.c.pysam.c:2144:9: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 2 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/samtools.pysam.c -o build/temp.linux-arm64-3.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam_view.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_import.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/cut_target.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/tmp_file.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_split.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_index.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_md.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sample.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/dict.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bamtk.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bedidx.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/padding.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/phase.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/faidx.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/stats.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam_header.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bedcov.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_color.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/stdio.h:867, from samtools/samtools.pysam.h:4, from samtools/sam_opts.c.pysam.c:1: In function ‘fprintf’, inlined from ‘parse_sam_global_opt’ at samtools/sam_opts.c.pysam.c:87:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:100:10: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 100 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/lz4/lz4.c -o build/temp.linux-arm64-3.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcsamtools.o build/temp.linux-arm64-3.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_markdup.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_sort.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-arm64-3.7/samtools/samtools.pysam.o build/temp.linux-arm64-3.7/samtools/sam_view.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_mate.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_import.c.pysam.o build/temp.linux-arm64-3.7/samtools/cut_target.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_aux.c.pysam.o build/temp.linux-arm64-3.7/samtools/tmp_file.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_stat.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_split.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_index.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_md.c.pysam.o build/temp.linux-arm64-3.7/samtools/sample.c.pysam.o build/temp.linux-arm64-3.7/samtools/dict.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam2bcf.c.pysam.o build/temp.linux-arm64-3.7/samtools/bamtk.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_reheader.c.pysam.o build/temp.linux-arm64-3.7/samtools/bedidx.c.pysam.o build/temp.linux-arm64-3.7/samtools/stats_isize.c.pysam.o build/temp.linux-arm64-3.7/samtools/padding.c.pysam.o build/temp.linux-arm64-3.7/samtools/phase.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam2depth.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-arm64-3.7/samtools/faidx.c.pysam.o build/temp.linux-arm64-3.7/samtools/stats.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam_header.c.pysam.o build/temp.linux-arm64-3.7/samtools/bedcov.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_cat.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam_utils.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-arm64-3.7/samtools/bamshuf.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_color.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_flags.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam_opts.c.pysam.o build/temp.linux-arm64-3.7/samtools/lz4/lz4.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) building 'pysam.libcbcftools' extension creating build/temp.linux-arm64-3.7/bcftools aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcbcftools.c -o build/temp.linux-arm64-3.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/reheader.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In function ‘realign’, inlined from ‘normalize_line’ at bcftools/vcfnorm.c.pysam.c:1719:23: bcftools/vcfnorm.c.pysam.c:347:17: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 347 | error("Non-ACGTN alternate allele at %s:%d .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bin.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/em.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/main.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/regidx.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/kmin.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/consensus.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/filter.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bcftools.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/prob1.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/ccall.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/hclust.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/mcall.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/convert.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/HMM.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/tabix.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:684:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 684 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:29, from /usr/include/htslib/vcf.h:40, from bcftools/vcfmerge.c.pysam.c:33: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/csq.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/version.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcbcftools.o build/temp.linux-arm64-3.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-3.7/bcftools/gvcf.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfsom.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfsort.c.pysam.o build/temp.linux-arm64-3.7/bcftools/reheader.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcffilter.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfview.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bam_sample.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bin.c.pysam.o build/temp.linux-arm64-3.7/bcftools/em.c.pysam.o build/temp.linux-arm64-3.7/bcftools/main.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfroh.c.pysam.o build/temp.linux-arm64-3.7/bcftools/regidx.c.pysam.o build/temp.linux-arm64-3.7/bcftools/kmin.c.pysam.o build/temp.linux-arm64-3.7/bcftools/ploidy.c.pysam.o build/temp.linux-arm64-3.7/bcftools/consensus.c.pysam.o build/temp.linux-arm64-3.7/bcftools/filter.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bcftools.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfindex.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-arm64-3.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-arm64-3.7/bcftools/prob1.c.pysam.o build/temp.linux-arm64-3.7/bcftools/ccall.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcmp.c.pysam.o build/temp.linux-arm64-3.7/bcftools/hclust.c.pysam.o build/temp.linux-arm64-3.7/bcftools/mpileup.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfquery.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfcall.c.pysam.o build/temp.linux-arm64-3.7/bcftools/mcall.c.pysam.o build/temp.linux-arm64-3.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfisec.c.pysam.o build/temp.linux-arm64-3.7/bcftools/convert.c.pysam.o build/temp.linux-arm64-3.7/bcftools/HMM.c.pysam.o build/temp.linux-arm64-3.7/bcftools/tabix.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfstats.c.pysam.o build/temp.linux-arm64-3.7/bcftools/csq.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-arm64-3.7/bcftools/version.c.pysam.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcutils.c' Cython extension (up-to-date) building 'pysam.libcutils' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcutils.c -o build/temp.linux-arm64-3.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6101:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration] 6101 | bcftools_set_stderr(__pyx_t_9); | ^~~~~~~~~~~~~~~~~~~ | samtools_set_stderr pysam/libcutils.c:6245:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration] 6245 | bcftools_set_stdout_fn(__pyx_t_12); | ^~~~~~~~~~~~~~~~~~~~~~ | samtools_set_stdout_fn pysam/libcutils.c:6256:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration] 6256 | bcftools_set_stdout(__pyx_t_9); | ^~~~~~~~~~~~~~~~~~~ | samtools_set_stdout pysam/libcutils.c:7011:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration] 7011 | bcftools_set_optind(1); | ^~~~~~~~~~~~~~~~~~~ | samtools_set_optind pysam/libcutils.c:7090:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration] 7090 | __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); | ^~~~~~~~~~~~~ | samtools_main pysam/libcutils.c:7159:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration] 7159 | bcftools_unset_stderr(); | ^~~~~~~~~~~~~~~~~~~~~ | samtools_unset_stderr pysam/libcutils.c:7195:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration] 7195 | bcftools_unset_stdout(); | ^~~~~~~~~~~~~~~~~~~~~ | samtools_unset_stdout pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:511:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] 511 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ pysam/libcutils.c:5833:7: note: ‘__pyx_v_retval’ was declared here 5833 | int __pyx_v_retval; | ^~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/pysam_util.c -o build/temp.linux-arm64-3.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcutils.o build/temp.linux-arm64-3.7/pysam/pysam_util.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcsamtools.cpython-37m-aarch64-linux-gnu -lcbcftools.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) building 'pysam.libcalignmentfile' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcalignmentfile.c -o build/temp.linux-arm64-3.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:29343:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] 29343 | __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); | ~^~~~~~~~~~~~~~~~~~~ | | | bam_pileup1_t ** {aka struct **} In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:604: /usr/include/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct **’} 686 | int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); | ~~~~~~~~~~~~~~~~~~~~~~^~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcalignmentfile.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) building 'pysam.libcsamfile' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcsamfile.c -o build/temp.linux-arm64-3.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcsamfile.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) building 'pysam.libcalignedsegment' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcalignedsegment.c -o build/temp.linux-arm64-3.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcalignedsegment.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabix.c' Cython extension (up-to-date) building 'pysam.libctabix' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libctabix.c -o build/temp.linux-arm64-3.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:8643:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 8643 | __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); | ^ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’: pysam/libctabix.c:13709:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 13709 | __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error) | ^~~~~~~~ pysam/libctabix.c:13741:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 13741 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error) | ^~~~~~~~ pysam/libctabix.c:14111:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 14111 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) | ^~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libctabix.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) building 'pysam.libcfaidx' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcfaidx.c -o build/temp.linux-arm64-3.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcfaidx.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbcf.c' Cython extension (up-to-date) building 'pysam.libcbcf' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcbcf.c -o build/temp.linux-arm64-3.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:32825:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] 32825 | __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen)); | ^~~~~~~~~~~~ In file included from pysam/htslib_util.h:5, from pysam/libcbcf.c:603: /usr/include/htslib/vcf.h:439:11: note: declared here 439 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcbcf.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) building 'pysam.libcbgzf' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcbgzf.c -o build/temp.linux-arm64-3.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcbgzf.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) building 'pysam.libctabixproxies' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libctabixproxies.c -o build/temp.linux-arm64-3.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libctabixproxies.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libcvcf' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.2+ds/samtools -I/<>/python-pysam-0.15.2+ds/samtools/lz4 -I/<>/python-pysam-0.15.2+ds/bcftools -I/<>/python-pysam-0.15.2+ds/pysam -I/<>/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcvcf.c -o build/temp.linux-arm64-3.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.0’: pysam/libcvcf.c:24840:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] 24840 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcvcf.o -L/<>/python-pysam-0.15.2+ds/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test make[1]: Entering directory '/<>/python-pysam-0.15.2+ds' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/<>/python-pysam-0.15.2+ds/tests/pysam_data' samtools faidx ex1.fa samtools import ex1.fa.fai ex1.sam.gz ex1.bam samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz [mpileup] 1 samples in 1 input files gunzip < ex1.sam.gz > ex1.sam samtools index ex1.bam samtools view -h ex1.bam | gzip > ex2.sam.gz gunzip < ex2.sam.gz > ex2.sam samtools view -bS ex2.sam > ex2.bam samtools index ex2.bam samtools calmd --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 gunzip < with_md.sam.gz > with_md.sam samtools view -bS with_md.sam > with_md.bam [W::bam_hdr_read] EOF marker is absent. The input is probably truncated samtools index with_md.bam samtools view -buS ex2.sam > uncompressed.bam samtools view -bS example_dash_in_chr.sam > example_dash_in_chr.bam samtools view -bS tag_bug.sam > tag_bug.bam samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam samtools view -bS softclip.sam > softclip.bam samtools view -bS example_empty_with_header.sam > example_empty_with_header.bam samtools view -bS test_unaligned.sam > test_unaligned.bam samtools view -bS ex9_fail.sam > ex9_fail.bam samtools view -bS ex10.sam > ex10.bam samtools view -bS example_aligned_pairs.sam > example_aligned_pairs.bam samtools view -bS example_empty_header.sam > example_empty_header.bam samtools view -bS ex9_nofail.sam > ex9_nofail.bam samtools view -bS issue100.sam > issue100.bam samtools view -bS ex5.sam > ex5.bam samtools view -bS example_reverse_complement.sam > example_reverse_complement.bam samtools view -bS ex6.sam > ex6.bam samtools view -bS rg_with_tab.sam > rg_with_tab.bam samtools view -bS ex_spliced.sam > ex_spliced.bam samtools view -bS example_btag.sam > example_btag.bam samtools view -bS test_query_position.sam > test_query_position.bam touch tmp.list samtools import tmp.list example_unmapped_reads_no_sq.sam example_unmapped_reads_no_sq.bam rm -f tmp.list samtools view -bS ex4.sam > ex4.bam samtools view -bS example_user_header.sam > example_user_header.bam samtools view -bS ex8.sam > ex8.bam samtools view -bS ex3.sam > ex3.bam samtools index example_dash_in_chr.bam samtools index tag_bug.bam samtools index test_mapped_unmapped.bam samtools index softclip.bam samtools index example_empty_with_header.bam samtools index test_unaligned.bam samtools index ex9_fail.bam samtools index ex10.bam samtools index example_aligned_pairs.bam samtools index example_empty_header.bam samtools index ex9_nofail.bam samtools index issue100.bam samtools index ex5.bam samtools index example_reverse_complement.bam samtools index ex6.bam samtools index rg_with_tab.bam samtools index ex_spliced.bam samtools index example_btag.bam samtools index test_query_position.bam samtools index example_unmapped_reads_no_sq.bam samtools index ex4.bam samtools index example_user_header.bam samtools index ex8.bam samtools index ex3.bam samtools view -bC -T ex1.fa ex1.sam > ex1.cram samtools view -bC -T ex1.fa ex2.sam > ex2.cram samtools view -bC -T ex1.fa ex3.sam > ex3.cram samtools index ex1.cram samtools index ex2.cram samtools index ex3.cram cp ex1.bam example_bai.bam samtools index example_bai.bam mv example_bai.bam.bai example_bai.bai head -c 124000 ex2.bam > ex2_truncated.bam grep "^@" ex2.sam | samtools view -Sb - > empty.bam samtools index empty.bam cp ex1.bam explicit_index.bam cp ex1.cram explicit_index.cram gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz bgzip < ex1.fa > ex1.fa.gz samtools faidx ex1.fa.gz cp ex1.bam ex1_csi.bam samtools index -c ex1_csi.bam rm with_md.sam make[2]: Leaving directory '/<>/python-pysam-0.15.2+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make all make[2]: Entering directory '/<>/python-pysam-0.15.2+ds/tests/cbcf_data' bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index bcftools index example_vcf42_withcontigs.vcf.gz # create csi index bgzip < example_vcf40.vcf > example_vcf40.vcf.gz tabix -p vcf example_vcf40.vcf.gz # create tbi index bcftools index example_vcf40.vcf.gz # create csi index bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz tabix -p vcf gnomad_fixed.vcf.gz # create tbi index bcftools index gnomad_fixed.vcf.gz # create csi index bgzip < gnomad.vcf > gnomad.vcf.gz tabix -p vcf gnomad.vcf.gz # create tbi index bcftools index gnomad.vcf.gz # create csi index bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz tabix -p vcf missing_genotypes.vcf.gz # create tbi index bcftools index missing_genotypes.vcf.gz # create csi index bgzip < example_vcf42.vcf > example_vcf42.vcf.gz tabix -p vcf example_vcf42.vcf.gz # create tbi index bcftools index example_vcf42.vcf.gz # create csi index bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index bcftools index example_vcf42_only_header.vcf.gz # create csi index bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf bcftools index example_vcf42_withcontigs.bcf bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf bcftools index example_vcf40.bcf bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools index gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools view -O b gnomad.vcf.gz -o gnomad.bcf bcftools index gnomad.bcf bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf bcftools index example_vcf42.bcf bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf bcftools index example_vcf42_only_header.bcf make[2]: Leaving directory '/<>/python-pysam-0.15.2+ds/tests/cbcf_data' dh_auto_test I: pybuild base:217: cd /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest tests ============================= test session starts ============================== platform linux2 -- Python 2.7.17, pytest-4.6.5, py-1.8.0, pluggy-0.13.0 -- /usr/bin/python2.7 cachedir: .pytest_cache rootdir: /<>/python-pysam-0.15.2+ds, inifile: setup.cfg collecting ... collected 926 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestCigar::testCigar PASSED tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testLongTags PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_eWaYxz PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_dv8Qea PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_HpzAiV PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_Hb2EdY PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0m7IGV PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_mJiGnH PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal SKIPPED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file missing_directory/new_file.bam PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/ex1.bam.bai PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing SKIPPED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/compile_test.py::BAMTest::testCount PASSED tests/compile_test.py::GTFTest::testCount PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage SKIPPED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =============================== warnings summary =============================== /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369 /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/_compile_test.pyx tree = Parsing.p_module(s, pxd, full_module_name) .pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py:1459: UserWarning: no BGZF EOF marker; file may be truncated ignore_truncation=True) -- Docs: https://docs.pytest.org/en/latest/warnings.html ============= 909 passed, 17 skipped, 2 warnings in 124.59 seconds ============= I: pybuild base:217: cd /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build; python3.8 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.8.0, pytest-4.6.5, py-1.8.0, pluggy-0.13.0 -- /usr/bin/python3.8 cachedir: .pytest_cache rootdir: /<>/python-pysam-0.15.2+ds, inifile: setup.cfg collecting ... collected 930 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestCigar::testCigar PASSED tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testLongTags PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_sjh8pq05 PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1gf_h2rh PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_5d89ym1x PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ia3i3cb7 PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_42wugelj PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_eo00gtd1 PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file missing_directory/new_file.bam PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/ex1.bam.bai PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/compile_test.py::BAMTest::testCount PASSED tests/compile_test.py::GTFTest::testCount PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage SKIPPED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestUnicode::testFromTabix PASSED tests/tabix_test.py::TestUnicode::testFromVCF PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =============================== warnings summary =============================== pysam/__init__.py:16 pysam/__init__.py:16 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.9 it will stop working import pysam.libcsamfile as libcsamfile /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369 /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/_compile_test.pyx tree = Parsing.p_module(s, pxd, full_module_name) tests/samtools_test.py:48 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/samtools_test.py:48: DeprecationWarning: invalid escape sequence \s x = re.search("Version:\s+(\S+)", lines).groups()[0] tests/samtools_test.py:192 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/samtools_test.py:192: DeprecationWarning: invalid escape sequence \( full_statement = re.sub("%\(out\)s", self.executable, statement) tests/samtools_test.py:202 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/samtools_test.py:202: DeprecationWarning: invalid escape sequence \( pysam_parts = [re.sub("%\(out\)s", "pysam", x) for x in parts[1:]] tests/samtools_test.py:275 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/samtools_test.py:275: DeprecationWarning: invalid escape sequence \s expected = "Usage:\s+{} {}".format(self.executable, command) tests/tabixproxies_test.py:131 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/tabixproxies_test.py:131: DeprecationWarning: invalid escape sequence \d s = re.sub("\"(\d+)\"", r"\1", s) .pybuild/cpython3_3.8_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/tests/AlignmentFile_test.py:1458: UserWarning: no BGZF EOF marker; file may be truncated s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex2_truncated.bam'), -- Docs: https://docs.pytest.org/en/latest/warnings.html ============= 920 passed, 10 skipped, 9 warnings in 117.62 seconds ============= I: pybuild base:217: cd /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build; python3.7 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.7.5, pytest-4.6.5, py-1.8.0, pluggy-0.13.0 -- /usr/bin/python3.7 cachedir: .pytest_cache rootdir: /<>/python-pysam-0.15.2+ds, inifile: setup.cfg collecting ... collected 930 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestCigar::testCigar PASSED tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testLongTags PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_utdrs5qd PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_q8ktj0ok PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_wyondk8f PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_5lw4lty4 PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_rjyvg228 PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_3_w2e7w8 PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file missing_directory/new_file.bam PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/ex1.bam.bai PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/compile_test.py::BAMTest::testCount PASSED tests/compile_test.py::GTFTest::testCount PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage SKIPPED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestUnicode::testFromTabix PASSED tests/tabix_test.py::TestUnicode::testFromVCF PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =============================== warnings summary =============================== pysam/__init__.py:16 pysam/__init__.py:16 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working import pysam.libcsamfile as libcsamfile /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369 /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/_compile_test.pyx tree = Parsing.p_module(s, pxd, full_module_name) tests/samtools_test.py:48 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/samtools_test.py:48: DeprecationWarning: invalid escape sequence \s x = re.search("Version:\s+(\S+)", lines).groups()[0] tests/samtools_test.py:192 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/samtools_test.py:192: DeprecationWarning: invalid escape sequence \( full_statement = re.sub("%\(out\)s", self.executable, statement) tests/samtools_test.py:202 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/samtools_test.py:202: DeprecationWarning: invalid escape sequence \( pysam_parts = [re.sub("%\(out\)s", "pysam", x) for x in parts[1:]] tests/samtools_test.py:275 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/samtools_test.py:275: DeprecationWarning: invalid escape sequence \s expected = "Usage:\s+{} {}".format(self.executable, command) tests/tabixproxies_test.py:131 /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tabixproxies_test.py:131: DeprecationWarning: invalid escape sequence \d s = re.sub("\"(\d+)\"", r"\1", s) .pybuild/cpython3_3.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/AlignmentFile_test.py:1459: UserWarning: no BGZF EOF marker; file may be truncated ignore_truncation=True) -- Docs: https://docs.pytest.org/en/latest/warnings.html ============= 920 passed, 10 skipped, 9 warnings in 120.76 seconds ============= make[1]: Leaving directory '/<>/python-pysam-0.15.2+ds' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python2,python3 --buildsystem=pybuild dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python2 setup.py install --root /<>/python-pysam-0.15.2+ds/debian/python-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install running build running build_py copying pysam/config.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) running install_lib creating /<>/python-pysam-0.15.2+ds/debian/python-pysam creating /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr creating /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib creating /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7 creating /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages creating /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/Pileup.pyc -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/cbcftools_util.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/samtools.py -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.pxd -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/Pileup.py -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/csamtools_util.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/__init__.pyc -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.pxd -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.pxd -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/samtools.pyc -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.pxd -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/version.py -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/htslib_util.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.pxd -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/config.pyc -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.pxd -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/__init__.py -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.pxd -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/pysam_util.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/bcftools.py -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/config.py -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.pxd -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/bcftools.pyc -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.pxd -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/utils.py -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/pysam_stream.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/version.pyc -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.pxd -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam creating /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include creating /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/config.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bedidx.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sample.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32/zlib.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32/xcurses.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32/zconf.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/stats_isize.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/samtools.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam2bcf.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/tmp_file.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam_opts.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam_header.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/version.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_endian.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/config.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bin.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bcftools.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/HMM.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/convert.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/kmin.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/mw.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/kheap.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/rbuf.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/filter.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/vcmp.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/call.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/prob1.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/gvcf.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/regidx.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/version.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/ploidy.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/hclust.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bam_sample.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/__init__.py -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/utils.pyc -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/log.txt -> /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages byte-compiling /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/samtools.py to samtools.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/Pileup.py to Pileup.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/version.py to version.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/__init__.py to __init__.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/bcftools.py to bcftools.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/config.py to config.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/utils.py to utils.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/__init__.py to __init__.pyc running install_egg_info running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/INSTALL' warning: no files found matching 'htslib/NEWS' warning: no previously-included files found matching 'htslib/config.h' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/htslib_vars.mk' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/config.mk.in' warning: no files found matching 'htslib/config.h.in' warning: no files found matching 'htslib/htslib.pc.in' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'htslib/os/*.c' warning: no files found matching 'htslib/os/*.h' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam-0.15.2.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:217: /usr/bin/python3.8 setup.py install --root /<>/python-pysam-0.15.2+ds/debian/python3-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install running build running build_py copying pysam/config.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) Fixing /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) running install_lib creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8 creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabix.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/cbcftools_util.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcftools.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcfaidx.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbgzf.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/samtools.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcf.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcf.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/Pileup.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamfile.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/csamtools_util.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcftools.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcvcf.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabix.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignedsegment.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamtools.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/version.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/htslib_util.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabixproxies.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcvcf.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcutils.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabixproxies.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/pysam_util.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignmentfile.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcutils.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/bcftools.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamtools.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcfaidx.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libchtslib.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/utils.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/pysam_stream.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamfile.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libchtslib.cpython-38-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/samtools.cpython-38.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/bcftools.cpython-38.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/__init__.cpython-38.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/utils.cpython-38.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/config.cpython-38.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/version.cpython-38.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/Pileup.cpython-38.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/config.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bedidx.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sample.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/win32/zlib.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/win32/xcurses.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/win32/zconf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/stats_isize.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/samtools.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam2bcf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/tmp_file.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sam_opts.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sam_header.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sam.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/version.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam_endian.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/config.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bin.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bcftools.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/HMM.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/convert.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/kmin.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/mw.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/kheap.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/rbuf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/filter.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/vcmp.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/call.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/prob1.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/gvcf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/regidx.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/version.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/ploidy.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/hclust.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bam_sample.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/__init__.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.8_pysam/build/log.txt -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/samtools.py to samtools.cpython-38.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/Pileup.py to Pileup.cpython-38.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/version.py to version.cpython-38.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/bcftools.py to bcftools.cpython-38.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/config.py to config.cpython-38.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/utils.py to utils.cpython-38.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/__init__.py to __init__.cpython-38.pyc running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/INSTALL' warning: no files found matching 'htslib/NEWS' warning: no previously-included files found matching 'htslib/config.h' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/htslib_vars.mk' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/config.mk.in' warning: no files found matching 'htslib/config.h.in' warning: no files found matching 'htslib/htslib.pc.in' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'htslib/os/*.c' warning: no files found matching 'htslib/os/*.h' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam-0.15.2.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:217: /usr/bin/python3 setup.py install --root /<>/python-pysam-0.15.2+ds/debian/python3-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install running build running build_py copying pysam/config.py -> /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) Fixing /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) running install_lib creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7 creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/cbcftools_util.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/csamtools_util.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/htslib_util.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/pysam_util.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/pysam_stream.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.pxd -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/utils.cpython-37.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/bcftools.cpython-37.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/version.cpython-37.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/__init__.cpython-37.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/Pileup.cpython-37.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/samtools.cpython-37.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/config.cpython-37.pyc -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/config.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bedidx.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sample.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32/zlib.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32/xcurses.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32/zconf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/stats_isize.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/samtools.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam2bcf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/tmp_file.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam_opts.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam_header.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/version.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_endian.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/config.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bin.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bcftools.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/HMM.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/convert.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/kmin.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/mw.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/kheap.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/rbuf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/filter.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/vcmp.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/call.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/prob1.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/gvcf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/regidx.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/version.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/ploidy.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/hclust.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bam_sample.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include copying /<>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/log.txt -> /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/samtools.py to samtools.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/Pileup.py to Pileup.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/version.py to version.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__init__.py to __init__.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/bcftools.py to bcftools.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/config.py to config.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/utils.py to utils.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/__init__.py to __init__.cpython-37.pyc running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/INSTALL' warning: no files found matching 'htslib/NEWS' warning: no previously-included files found matching 'htslib/config.h' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/htslib_vars.mk' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/config.mk.in' warning: no files found matching 'htslib/config.h.in' warning: no files found matching 'htslib/htslib.pc.in' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'htslib/os/*.c' warning: no files found matching 'htslib/os/*.h' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam-0.15.2.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/<>/python-pysam-0.15.2+ds' cd tests/pysam_data && /usr/bin/make clean make[2]: Entering directory '/<>/python-pysam-0.15.2+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ with_md.sam.gz \ *.fq.gz make[2]: Leaving directory '/<>/python-pysam-0.15.2+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[2]: Entering directory '/<>/python-pysam-0.15.2+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[2]: Leaving directory '/<>/python-pysam-0.15.2+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete #find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully find . -name "*.bai*" -delete find . -name "*.cram*" -delete #find . -name "*.bam" -delete # which deletes files tested rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh_install -Xtest.gtf.gz find debian -name log.txt -delete make[1]: Leaving directory '/<>/python-pysam-0.15.2+ds' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_python2 -a -O--buildsystem=pybuild I: dh_python2 fs:343: renaming libcalignedsegment.so to libcalignedsegment.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcalignmentfile.so to libcalignmentfile.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcbcf.so to libcbcf.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcbcftools.so to libcbcftools.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcbgzf.so to libcbgzf.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcfaidx.so to libcfaidx.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libchtslib.so to libchtslib.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcsamfile.so to libcsamfile.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcsamtools.so to libcsamtools.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libctabix.so to libctabix.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libctabixproxies.so to libctabixproxies.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcutils.so to libcutils.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcvcf.so to libcvcf.aarch64-linux-gnu.so dh_python3 -a -O--buildsystem=pybuild dh_installinit -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-pysam: substitution variable ${python:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python-pysam: substitution variable ${python:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing python3-pysam (in debian/python3-pysam); do_strip: , oemstrip: pkgstriptranslations: processing python3-pysam-dbgsym (in debian/.debhelper/python3-pysam/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python-pysam (in debian/python-pysam); do_strip: , oemstrip: pkgstriptranslations: processing python-pysam-dbgsym (in debian/.debhelper/python-pysam/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-pysam/DEBIAN/control, package python3-pysam, directory debian/python3-pysam pkgstripfiles: processing control file: debian/.debhelper/python-pysam/dbgsym-root/DEBIAN/control, package python-pysam-dbgsym, directory debian/.debhelper/python-pysam/dbgsym-root dpkg-deb: building package 'python-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python-pysam/python-pysam-dbgsym_0.15.2+ds-2build1_arm64.deb'. INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/python3-pysam/dbgsym-root/DEBIAN/control, package python3-pysam-dbgsym, directory debian/.debhelper/python3-pysam/dbgsym-root dpkg-deb: building package 'python3-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-pysam/python3-pysam-dbgsym_0.15.2+ds-2build1_arm64.deb'. INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... Renaming python-pysam-dbgsym_0.15.2+ds-2build1_arm64.deb to python-pysam-dbgsym_0.15.2+ds-2build1_arm64.ddeb INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python-pysam/DEBIAN/control, package python-pysam, directory debian/python-pysam pkgstripfiles: Truncating usr/share/doc/python-pysam/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pysam ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-pysam' in '../python-pysam_0.15.2+ds-2build1_arm64.deb'. pkgstripfiles: Truncating usr/share/doc/python3-pysam/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pysam ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.15.2+ds-2build1_arm64.deb'. Renaming python3-pysam-dbgsym_0.15.2+ds-2build1_arm64.deb to python3-pysam-dbgsym_0.15.2+ds-2build1_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../python-pysam_0.15.2+ds-2build1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20191020-2214 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-pysam_0.15.2+ds-2build1_arm64.changes: --------------------------------------------- Format: 1.8 Date: Fri, 18 Oct 2019 18:43:39 +0000 Source: python-pysam Binary: python-pysam python3-pysam Architecture: arm64 Version: 0.15.2+ds-2build1 Distribution: focal-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose Description: python-pysam - interface for the SAM/BAM sequence alignment and mapping format ( python3-pysam - interface for the SAM/BAM sequence alignment and mapping format ( Changes: python-pysam (0.15.2+ds-2build1) focal; urgency=medium . * No-change rebuild to build with python3.8. Checksums-Sha1: ef53318f2094cfcd497c06f93f8a6226e86dcb74 6372820 python-pysam-dbgsym_0.15.2+ds-2build1_arm64.ddeb 79ef3fc9e2c6e902b84c8c89153b1b864133fc5a 9952 python-pysam_0.15.2+ds-2build1_arm64.buildinfo b96bb2829f3c895c260f28de915eda31e0af86b8 1499480 python-pysam_0.15.2+ds-2build1_arm64.deb 31831766c1d83719fa838f58bbe1ff4afad51ab9 15741832 python3-pysam-dbgsym_0.15.2+ds-2build1_arm64.ddeb f90ebeb4f3787f403dc45b2f341ee80d0a9669cd 2318776 python3-pysam_0.15.2+ds-2build1_arm64.deb Checksums-Sha256: f909b7df6df45f100adea9ef7ec3f2a7dca4a30372a947ceda84b83bc92c43d8 6372820 python-pysam-dbgsym_0.15.2+ds-2build1_arm64.ddeb a192391aa6fcf491a32ca1ea3238008b6bbd28301c96c3f24fe09d7c22230c9e 9952 python-pysam_0.15.2+ds-2build1_arm64.buildinfo 1ce548f4eeef7f0af6ffb41c8eed2d57cdfaca33b60209430fd560c20e19a06d 1499480 python-pysam_0.15.2+ds-2build1_arm64.deb 82db749a174979a58d83463e4a7cb2b0a59e3c157cf6274a069c672ab6c07bdb 15741832 python3-pysam-dbgsym_0.15.2+ds-2build1_arm64.ddeb 52e2a5c9ea1ff03ed4c84cd6a2b89fe263b4f4c4fa368ecf3ccae7bce6def4b1 2318776 python3-pysam_0.15.2+ds-2build1_arm64.deb Files: eff0c9d594ea15848ad73f4f39d9a8d3 6372820 debug optional python-pysam-dbgsym_0.15.2+ds-2build1_arm64.ddeb 2dc1de412d9c19e43e7e8f7774909012 9952 python optional python-pysam_0.15.2+ds-2build1_arm64.buildinfo 2f5dcd72ed2fca4832ccc0786671d79b 1499480 python optional python-pysam_0.15.2+ds-2build1_arm64.deb 380cf7bc06ce61b9a7c3437333677cd1 15741832 debug optional python3-pysam-dbgsym_0.15.2+ds-2build1_arm64.ddeb b228c919a04b9432040af48a795dfeb8 2318776 python optional python3-pysam_0.15.2+ds-2build1_arm64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python-pysam_0.15.2+ds-2build1_arm64.deb ---------------------------------------- new debian package, version 2.0. size 1499480 bytes: control archive=3292 bytes. 810 bytes, 17 lines control 8538 bytes, 89 lines md5sums 162 bytes, 9 lines * postinst #!/bin/sh 263 bytes, 14 lines * prerm #!/bin/sh Package: python-pysam Version: 0.15.2+ds-2build1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 5863 Depends: libc6 (>= 2.17), libhts2 (>= 1.9), zlib1g (>= 1:1.1.4), python2 (<< 2.8), python2 (>= 2.7~), python2:any (<< 2.8), python2:any (>= 2.7~) Provides: python2.7-pysam Section: python Priority: optional Homepage: http://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2) Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. . This package installs the module for Python 2. drwxr-xr-x root/root 0 2019-10-18 18:43 ./ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/lib/ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/lib/python2.7/ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/lib/python2.7/dist-packages/ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/lib/python2.7/dist-packages/pysam-0.15.2.egg-info/ -rw-r--r-- root/root 1588 2019-10-18 18:43 ./usr/lib/python2.7/dist-packages/pysam-0.15.2.egg-info/PKG-INFO -rw-r--r-- root/root 1 2019-10-18 18:43 ./usr/lib/python2.7/dist-packages/pysam-0.15.2.egg-info/dependency_links.txt -rw-r--r-- root/root 1 2019-10-18 18:43 ./usr/lib/python2.7/dist-packages/pysam-0.15.2.egg-info/not-zip-safe -rw-r--r-- root/root 6 2019-10-18 18:43 ./usr/lib/python2.7/dist-packages/pysam-0.15.2.egg-info/top_level.txt drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/lib/python2.7/dist-packages/pysam/ -rw-r--r-- root/root 8975 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/Pileup.py -rw-r--r-- root/root 3235 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/__init__.py -rw-r--r-- root/root 428 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/bcftools.py -rw-r--r-- root/root 102 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/cbcftools_util.h -rw-r--r-- root/root 16 2019-10-18 18:43 ./usr/lib/python2.7/dist-packages/pysam/config.py -rw-r--r-- root/root 102 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/csamtools_util.h -rw-r--r-- root/root 3070 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/htslib_util.h drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/lib/python2.7/dist-packages/pysam/include/ -rw-r--r-- root/root 0 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/include/__init__.py drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/ -rw-r--r-- root/root 5022 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/HMM.h -rw-r--r-- root/root 5089 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/bam2bcf.h -rw-r--r-- root/root 2030 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/bam_sample.h -rw-r--r-- root/root 3155 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/bcftools.h -rw-r--r-- root/root 1021 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/bcftools.pysam.h -rw-r--r-- root/root 2188 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/bin.h -rw-r--r-- root/root 4689 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/call.h -rw-r--r-- root/root 77 2019-10-18 18:43 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/config.h -rw-r--r-- root/root 1751 2019-01-10 22:35 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/convert.h -rw-r--r-- root/root 1982 2019-01-10 22:35 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./usr/share/doc/python-pysam/copyright drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/share/lintian/ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 211 2019-01-16 09:47 ./usr/share/lintian/overrides/python-pysam python3-pysam_0.15.2+ds-2build1_arm64.deb ----------------------------------------- new debian package, version 2.0. size 2318776 bytes: control archive=3672 bytes. 775 bytes, 17 lines control 10009 bytes, 102 lines md5sums 252 bytes, 12 lines * postinst #!/bin/sh 401 bytes, 12 lines * prerm #!/bin/sh Package: python3-pysam Source: python-pysam Version: 0.15.2+ds-2build1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 11203 Depends: libc6 (>= 2.17), libhts2 (>= 1.9), zlib1g (>= 1:1.1.4), python3 (<< 3.9), python3 (>= 3.7~), python3:any Section: python Priority: optional Homepage: http://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3) Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. . This package installs the module for Python 3. drwxr-xr-x root/root 0 2019-10-18 18:43 ./ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/lib/ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/lib/python3/ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/lib/python3/dist-packages/pysam-0.15.2.egg-info/ -rw-r--r-- root/root 1588 2019-10-18 18:43 ./usr/lib/python3/dist-packages/pysam-0.15.2.egg-info/PKG-INFO -rw-r--r-- root/root 1 2019-10-18 18:43 ./usr/lib/python3/dist-packages/pysam-0.15.2.egg-info/dependency_links.txt -rw-r--r-- root/root 1 2019-10-18 18:43 ./usr/lib/python3/dist-packages/pysam-0.15.2.egg-info/not-zip-safe -rw-r--r-- root/root 6 2019-10-18 18:43 ./usr/lib/python3/dist-packages/pysam-0.15.2.egg-info/top_level.txt drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/lib/python3/dist-packages/pysam/ -rw-r--r-- root/root 8975 2019-01-10 22:35 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2019-10-18 18:43 ./usr/share/ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/share/doc/python3-pysam/ -rw-r--r-- root/root 1558 2019-10-18 18:43 ./usr/share/doc/python3-pysam/changelog.Debian.gz -rw-r--r-- root/root 6348 2019-01-16 09:47 ./usr/share/doc/python3-pysam/copyright drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/share/lintian/ drwxr-xr-x root/root 0 2019-10-18 18:43 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 209 2019-01-16 09:47 ./usr/share/lintian/overrides/python3-pysam +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 439284 Build-Time: 2405 Distribution: focal-proposed Host Architecture: arm64 Install-Time: 88 Job: python-pysam_0.15.2+ds-2build1.dsc Machine Architecture: arm64 Package: python-pysam Package-Time: 2496 Source-Version: 0.15.2+ds-2build1 Space: 439284 Status: successful Version: 0.15.2+ds-2build1 -------------------------------------------------------------------------------- Finished at 20191020-2214 Build needed 00:41:36, 439284k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-17940056 Scanning for processes to kill in build PACKAGEBUILD-17940056