https://launchpad.net/ubuntu/+source/python-pysam/0.20.0+ds-1/+build/24884798 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-081 5.4.0-132-generic #148-Ubuntu SMP Mon Oct 17 16:02:06 UTC 2022 x86_64 Buildd toolchain package versions: launchpad-buildd_223~593~ubuntu20.04.1 python3-lpbuildd_223~593~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.6 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 30 Nov 05:28:05 ntpdate[1800]: adjust time server 10.131.248.1 offset -0.000968 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24884798 --image-type chroot /home/buildd/filecache-default/b509365b3a13e4aa6176e31a361b75cab8d51910 Creating target for build PACKAGEBUILD-24884798 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24884798 Starting target for build PACKAGEBUILD-24884798 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24884798 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-24884798 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24884798 Updating target for build PACKAGEBUILD-24884798 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [259 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main amd64 Packages [1393 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe amd64 Packages [14.6 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5841 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 Packages [327 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [119 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 Packages [1724 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [667 kB] Fetched 25.7 MB in 3s (9381 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: libperl5.34 perl-modules-5.34 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.36 perl-modules-5.36 The following packages will be upgraded: adduser advancecomp apt binutils binutils-common binutils-x86-64-linux-gnu debconf debianutils e2fsprogs fakeroot gpg gpg-agent gpgconf gpgv grep init init-system-helpers libapparmor1 libapt-pkg6.0 libassuan0 libaudit-common libaudit1 libbinutils libcap-ng0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libext2fs2 libfakeroot libffi8 libgpg-error0 libgprofng0 libgssapi-krb5-2 libip4tc2 libjson-c5 libk5crypto3 libkrb5-3 libkrb5support0 liblz4-1 liblzma5 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpng16-16 libreadline8 libseccomp2 libselinux1 libsqlite3-0 libss2 libssl3 linux-libc-dev login logsave openssl passwd perl perl-base pinentry-curses readline-common tar usrmerge xz-utils zlib1g 67 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 28.1 MB of archives. After this operation, 46.5 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 debianutils amd64 5.7-0.4 [103 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 grep amd64 3.8-3 [159 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main amd64 login amd64 1:4.13+dfsg1-1ubuntu1 [199 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 perl-modules-5.36 all 5.36.0-4ubuntu2 [2984 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libperl5.36 amd64 5.36.0-4ubuntu2 [4808 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 perl amd64 5.36.0-4ubuntu2 [235 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 perl-base amd64 5.36.0-4ubuntu2 [1779 kB] Get:8 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcrypt-dev amd64 1:4.4.33-1 [113 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcrypt1 amd64 1:4.4.33-1 [80.8 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu2 [61.1 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main amd64 tar amd64 1.34+dfsg-1.1 [292 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main amd64 usrmerge all 33ubuntu1 [57.0 kB] Get:13 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 init-system-helpers all 1.65.2 [38.1 kB] Get:14 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 liblz4-1 amd64 1.9.4-1 [63.1 kB] Get:15 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 liblzma5 amd64 5.2.8-0.0 [102 kB] Get:16 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libapt-pkg6.0 amd64 2.5.4 [902 kB] Get:17 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libaudit-common all 1:3.0.7-1ubuntu2 [5018 B] Get:18 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcap-ng0 amd64 0.8.3-1build1 [15.2 kB] Get:19 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libaudit1 amd64 1:3.0.7-1ubuntu2 [45.4 kB] Get:20 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 debconf all 1.5.80 [125 kB] Get:21 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpam0g amd64 1.5.2-5ubuntu1 [60.2 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libselinux1 amd64 3.4-1build1 [77.9 kB] Get:23 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpam-modules-bin amd64 1.5.2-5ubuntu1 [45.5 kB] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpam-modules amd64 1.5.2-5ubuntu1 [282 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main amd64 passwd amd64 1:4.13+dfsg1-1ubuntu1 [842 kB] Get:26 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 adduser all 3.129ubuntu1 [59.0 kB] Get:27 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgpg-error0 amd64 1.46-1 [68.9 kB] Get:28 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpgv amd64 2.2.40-1ubuntu1 [137 kB] Get:29 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libseccomp2 amd64 2.5.4-1ubuntu2 [46.2 kB] Get:30 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 apt amd64 2.5.4 [1378 kB] Get:31 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 logsave amd64 1.46.6~rc1-1ubuntu1 [10.5 kB] Get:32 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libext2fs2 amd64 1.46.6~rc1-1ubuntu1 [207 kB] Get:33 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 e2fsprogs amd64 1.46.6~rc1-1ubuntu1 [590 kB] Get:34 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 init amd64 1.65.2 [4808 B] Get:35 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpam-runtime all 1.5.2-5ubuntu1 [40.0 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libffi8 amd64 3.4.4-1 [23.8 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcom-err2 amd64 1.46.6~rc1-1ubuntu1 [9650 B] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libss2 amd64 1.46.6~rc1-1ubuntu1 [12.2 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libapparmor1 amd64 3.0.7-1ubuntu4 [36.7 kB] Get:40 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libjson-c5 amd64 0.16-2 [32.8 kB] Get:41 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libssl3 amd64 3.0.5-2ubuntu2 [1893 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main amd64 libcryptsetup12 amd64 2:2.5.0-6ubuntu1 [222 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgssapi-krb5-2 amd64 1.20.1-1 [142 kB] Get:44 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libkrb5-3 amd64 1.20.1-1 [346 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libkrb5support0 amd64 1.20.1-1 [31.4 kB] Get:46 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libk5crypto3 amd64 1.20.1-1 [81.1 kB] Get:47 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libip4tc2 amd64 1.8.7-1ubuntu7 [19.7 kB] Get:48 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 readline-common all 8.2-1.2 [55.2 kB] Get:49 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libreadline8 amd64 8.2-1.2 [150 kB] Get:50 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsqlite3-0 amd64 3.40.0-1 [653 kB] Get:51 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 openssl amd64 3.0.5-2ubuntu2 [1178 kB] Get:52 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpng16-16 amd64 1.6.39-1 [186 kB] Get:53 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 xz-utils amd64 5.2.8-0.0 [142 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main amd64 advancecomp amd64 2.4-1 [180 kB] Get:55 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libctf-nobfd0 amd64 2.39-8ubuntu2 [99.9 kB] Get:56 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgprofng0 amd64 2.39-8ubuntu2 [897 kB] Get:57 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libctf0 amd64 2.39-8ubuntu2 [97.4 kB] Get:58 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.39-8ubuntu2 [2402 kB] Get:59 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libbinutils amd64 2.39-8ubuntu2 [610 kB] Get:60 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 binutils amd64 2.39-8ubuntu2 [3240 B] Get:61 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 binutils-common amd64 2.39-8ubuntu2 [233 kB] Get:62 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libfakeroot amd64 1.30.1-1ubuntu1 [30.9 kB] Get:63 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 fakeroot amd64 1.30.1-1ubuntu1 [60.1 kB] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libassuan0 amd64 2.5.5-5 [37.2 kB] Get:65 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 pinentry-curses amd64 1.2.1-1ubuntu1 [34.6 kB] Get:66 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpg amd64 2.2.40-1ubuntu1 [523 kB] Get:67 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpgconf amd64 2.2.40-1ubuntu1 [93.8 kB] Get:68 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpg-agent amd64 2.2.40-1ubuntu1 [217 kB] Get:69 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 linux-libc-dev amd64 5.19.0-23.24 [1345 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.1 MB in 0s (135 MB/s) (Reading database ... 13556 files and directories currently installed.) 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24884798 amd64 lunar-proposed -c chroot:build-PACKAGEBUILD-24884798 --arch=amd64 --dist=lunar-proposed --nolog -A python-pysam_0.20.0+ds-1.dsc Initiating build PACKAGEBUILD-24884798 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-132-generic #148-Ubuntu SMP Mon Oct 17 16:02:06 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-081.buildd +==============================================================================+ | python-pysam 0.20.0+ds-1 (amd64) Wed, 30 Nov 2022 05:28:22 +0000 | +==============================================================================+ Package: python-pysam Version: 0.20.0+ds-1 Source Version: 0.20.0+ds-1 Distribution: lunar-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24884798/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-9Sm0IN/resolver-Dc8RdA' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.20.0+ds-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-pysam-9Sm0IN/python-pysam-0.20.0+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-9Sm0IN' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.14~), zlib1g-dev, python3-dev, python3-setuptools, cython3, tabix, samtools, bcftools, python3-pytest, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.14~), zlib1g-dev, python3-dev, python3-setuptools, cython3, tabix, samtools, bcftools, python3-pytest, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [454 B] Get:5 copy:/<>/apt_archive ./ Packages [525 B] Fetched 1936 B in 0s (191 kB/s) Reading package lists... Reading package lists... Install main 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: libperl5.34 perl-modules-5.34 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu71 libjs-jquery libjs-sphinxdoc libjs-underscore libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libpipeline1 libpsl5 libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3 python3-attr python3-dev python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pyparsing python3-pytest python3-setuptools python3-tomli python3.10 python3.10-dev python3.10-minimal samtools tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc python3-numpy python3-matplotlib texlive-latex-recommended cython-doc dh-make flit python3-build python3-installer gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-attr-doc subversion python-pyparsing-doc python-setuptools-doc python3.10-venv python3.10-doc binfmt-support cwltool Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python3-pygments The following NEW packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu71 libjs-jquery libjs-sphinxdoc libjs-underscore libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libpipeline1 libpsl5 libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3 python3-attr python3-dev python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pyparsing python3-pytest python3-setuptools python3-tomli python3.10 python3.10-dev python3.10-minimal samtools sbuild-build-depends-main-dummy tabix zlib1g-dev 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 45.6 MB of archives. After this operation, 159 MB of additional disk space will be used. 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Get:80 http://ftpmaster.internal/ubuntu lunar/universe amd64 python3-pluggy all 1.0.0+repack-1 [15.1 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/universe amd64 python3-py all 1.11.0-1 [73.2 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/universe amd64 python3-tomli all 2.0.1-1 [16.6 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/universe amd64 python3-pytest all 7.1.2-2ubuntu1 [219 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main amd64 python3-setuptools all 59.6.0-1.2 [339 kB] Get:85 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 samtools amd64 1.16.1-1 [551 kB] Get:86 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 tabix amd64 1.16+ds-3 [488 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main amd64 dh-exec amd64 0.27 [25.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 45.6 MB in 0s (113 MB/s) Selecting previously unselected package libpython3.10-minimal:amd64. 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Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libpython3.10-stdlib:amd64 (3.10.8-3) ... Setting up dh-autoreconf (20) ... Setting up libjs-sphinxdoc (4.5.0-4) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14+20220924-2) ... Setting up groff-base (1.22.4-9) ... Setting up debugedit (1:5.0-5) ... Setting up libpython3-stdlib:amd64 (3.10.6-1ubuntu1) ... Setting up libpython3.10:amd64 (3.10.8-3) ... Setting up python3.10 (3.10.8-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:amd64 (7.86.0-2) ... Setting up python3 (3.10.6-1ubuntu1) ... Setting up libcurl4-gnutls-dev (7.86.0-2) ... Setting up man-db (2.11.1-1) ... 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-pyparsing (3.0.7-3) ... Setting up cython3 (0.29.32-1ubuntu1) ... Setting up libpython3.10-dev:amd64 (3.10.8-3) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up python3.10-dev (3.10.8-3) ... Setting up python3-lib2to3 (3.10.8-1) ... Setting up python3-pkg-resources (59.6.0-1.2) ... Setting up python3-distutils (3.10.8-1) ... Setting up dh-python (5.20221122) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.1.0-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libpython3-dev:amd64 (3.10.6-1ubuntu1) ... Setting up python3-setuptools (59.6.0-1.2) ... Setting up python3-tomli (2.0.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up bcftools (1.16-1) ... Setting up libhts-dev:amd64 (1.16+ds-3) ... Setting up debhelper (13.10.1ubuntu1) ... Setting up dh-exec (0.27) ... Setting up samtools (1.16.1-1) ... Setting up python3-packaging (21.3-1.1) ... Setting up python3-dev (3.10.6-1ubuntu1) ... Setting up python3-pytest (7.1.2-2ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (251.4-1ubuntu7) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-132-generic #148-Ubuntu SMP Mon Oct 17 16:02:06 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.39-8ubuntu2 dpkg-dev_1.21.9ubuntu1 g++-12_12.2.0-9ubuntu1 gcc-12_12.2.0-9ubuntu1 libc6-dev_2.36-0ubuntu4 libstdc++-12-dev_12.2.0-9ubuntu1 libstdc++6_12.2.0-9ubuntu1 linux-libc-dev_5.19.0-23.24 Package versions: adduser_3.129ubuntu1 advancecomp_2.4-1 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2-1ubuntu2 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logsave_1.46.6~rc1-1ubuntu1 lsb-base_11.2ubuntu1 lto-disabled-list_36 m4_1.4.19-1 make_4.3-4.1build1 man-db_2.11.1-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38-4ubuntu1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 openssl_3.0.5-2ubuntu2 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-4ubuntu2 perl-base_5.36.0-4ubuntu2 perl-modules-5.34_5.34.0-5ubuntu1 perl-modules-5.36_5.36.0-4ubuntu2 pinentry-curses_1.2.1-1ubuntu1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:3.3.17-7ubuntu1 python3_3.10.6-1ubuntu1 python3-attr_22.1.0-1 python3-dev_3.10.6-1ubuntu1 python3-distutils_3.10.8-1 python3-iniconfig_1.1.1-2 python3-lib2to3_3.10.8-1 python3-minimal_3.10.6-1ubuntu1 python3-more-itertools_8.10.0-2 python3-packaging_21.3-1.1 python3-pkg-resources_59.6.0-1.2 python3-pluggy_1.0.0+repack-1 python3-py_1.11.0-1 python3-pyparsing_3.0.7-3 python3-pytest_7.1.2-2ubuntu1 python3-setuptools_59.6.0-1.2 python3-tomli_2.0.1-1 python3.10_3.10.8-3 python3.10-dev_3.10.8-3 python3.10-minimal_3.10.8-3 readline-common_8.2-1.2 rpcsvc-proto_1.4.2-0ubuntu6 samtools_1.16.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 systemd_251.4-1ubuntu7 systemd-sysv_251.4-1ubuntu7 sysvinit-utils_3.04-1ubuntu1 tabix_1.16+ds-3 tar_1.34+dfsg-1.1 tzdata_2022f-0ubuntu2 ubuntu-keyring_2021.03.26 usrmerge_33ubuntu1 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 xz-utils_5.2.8-0.0 zlib1g_1:1.2.13.dfsg-1ubuntu2 zlib1g-dev_1:1.2.13.dfsg-1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-pysam Binary: python3-pysam, python-pysam-tests Architecture: any all Version: 0.20.0+ds-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://pysam.readthedocs.org/en/latest Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/python-pysam Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.14~), zlib1g-dev, python3-dev, python3-setuptools, cython3, tabix , samtools , bcftools , python3-pytest Package-List: python-pysam-tests deb python optional arch=all python3-pysam deb python optional arch=any Checksums-Sha1: 1a82c944f5d4269a999dc825401a1b5d7c1d87fd 1410696 python-pysam_0.20.0+ds.orig.tar.xz c63ea8c4802cfbd3f9c490b1332ca4fa1870d855 9864 python-pysam_0.20.0+ds-1.debian.tar.xz Checksums-Sha256: 173795398967fb1f776811965a48af6e46ecc7f53fc863ae53e8c57fe0068142 1410696 python-pysam_0.20.0+ds.orig.tar.xz 0028966e91f0b0e4b685a1e9679c67b2eb84822e7e91ca9008d9339e10c1c290 9864 python-pysam_0.20.0+ds-1.debian.tar.xz Files: 247ff229711954949de58a1cac767d9b 1410696 python-pysam_0.20.0+ds.orig.tar.xz ec4eb7fd7e87ea213850e046427361e3 9864 python-pysam_0.20.0+ds-1.debian.tar.xz Dgit: c8b92d7b81cfd24e8e4e18617e11dbc8d9203d98 debian archive/debian/0.20.0+ds-1 https://git.dgit.debian.org/python-pysam -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmOGeC0UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoxww//XhFJ8BgSDzDd+trk4kW25qO4s2Tx nOETYnBZ6n3zGncUtJHzVy4eu7bZNi1+v0Law7KcXAXQWXZwL5QNwyDFWrSoAndk 4/OwnZAZoSu5i112bkW+/+WXgRfcrCvRGi/OKSNWON1IxhtC0nvkRXrQf5OHQ6xl ac4T3hbRDc7lgirGvs/LJ1oEV2ENhCdqhRjWnIQFMGsYkSvgGzqHzBl1CAk/yJ+S ZmxL4x9hI/W/3GQ9JT2R4zGzK4jfG6bgXa4vyFm05G5D2iv56G1eMb0p6vdbB0nd WHWSou4CNEgg2gUE2nn34THqgz3xe7LzwGfMaUGt++ZsEFa2bP7Qypmy1NyzbeXu qGSe4k7BbOflnAhSVYYuwwXnUyUjMP9nEtklET6TJ5iqLUxBKK/5LHp1J1i59qMV Y2D+z8gKofDcDXNCiaFmUMW0fkFfzzAC8NpBhBY9MLDEuUDTDRezvagVbuZgVrFs BpbSEmYz6gK6GCMDnVNJxFdlScbKCJEleds1dctGYy8xgs9vhXsuSCtmZxDwY3CF oMytTETCgq7tG5P4P/JOe2ZBzfWdZTPzfKU1Ev1uy7BYB6PXCejQwz6o/lJqK03x A3iODKrooew0XdXUQFGSQWUnCkaT8nWdLLj2IikK3uiM5sXas0UR88QLXXZbYZ/H 4MYDVCylj0RC4eQ= =bdG0 -----END PGP SIGNATURE----- gpgv: Signature made Tue Nov 29 21:22:53 2022 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./python-pysam_0.20.0+ds-1.dsc dpkg-source: info: extracting python-pysam in /<> dpkg-source: info: unpacking python-pysam_0.20.0+ds.orig.tar.xz dpkg-source: info: unpacking python-pysam_0.20.0+ds-1.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 clean_less dpkg-source: info: applying skip-test-on-32-bit.patch Check disk 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-24884798 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24884798 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24884798 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.20.0+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/<>/tests/pysam_data' rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz make[1]: Leaving directory '/<>/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/<>/tests/cbcf_data' rm -f all.stamp *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/<>/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete 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 python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean I: pybuild base:240: python3.10 setup.py clean /<>/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils import log # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/.pybuild/cpython3_3.10_pysam/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.10' 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 '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.10 setup.py config /<>/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils import log # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build /<>/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils import log # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/Pileup.py -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/bcftools.py -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/__init__.py -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/version.py -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/utils.py -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/samtools.py -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/config.py -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam creating /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/.pybuild/cpython3_3.10_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) copying pysam/libcalignedsegment.pxd -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcsamtools.pxd -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libchtslib.pxd -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcbcf.pxd -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/pysam_util.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/cbcftools_util.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/htslib_util.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/version.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/py.typed -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcbcftools.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libctabixproxies.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcbcf.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libctabix.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcsamfile.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcalignmentfile.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libchtslib.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcsamtools.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcfaidx.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcbgzf.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcutils.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcvcf.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcalignedsegment.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/version.pyi -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam creating /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/consensus_pileup.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/config.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/splaysort.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/sample.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools creating /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/str_finder.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/utlist.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/variantkey.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/abuf.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/dbuf.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/cols.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/hex.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/dist.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/extsort.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c /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: /<>/pysam/libchtslib.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c /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: /<>/pysam/libcsamtools.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c /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: /<>/pysam/libcbcftools.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcutils.pyx to pysam/libcutils.c /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: /<>/pysam/libcutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c /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: /<>/pysam/libcalignmentfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcalignmentfile.pyx:2573:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2578:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2583:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2622:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2627:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2632:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c /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: /<>/pysam/libcsamfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c /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: /<>/pysam/libcalignedsegment.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libctabix.pyx to pysam/libctabix.c /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: /<>/pysam/libctabix.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c /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: /<>/pysam/libcfaidx.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbcf.pyx to pysam/libcbcf.c /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: /<>/pysam/libcbcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c /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: /<>/pysam/libcbgzf.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c /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: /<>/pysam/libctabixproxies.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcvcf.pyx to pysam/libcvcf.c /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: /<>/pysam/libcvcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libchtslib' extension creating build creating build/temp.linux-x86_64-3.10 creating build/temp.linux-x86_64-3.10/pysam x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/htslib_util.c -o build/temp.linux-x86_64-3.10/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.10/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/htslib_util.o build/temp.linux-x86_64-3.10/pysam/libchtslib.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libchtslib.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension building 'pysam.libcsamtools' extension creating build/temp.linux-x86_64-3.10/samtools creating build/temp.linux-x86_64-3.10/samtools/lz4 x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libcsamtools.c -o build/temp.linux-x86_64-3.10/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_color.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_import.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_index.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_md.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_split.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bamtk.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bedcov.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/bedidx.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/coverage.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/cut_target.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/dict.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/faidx.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/lz4/lz4.c -o build/temp.linux-x86_64-3.10/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/padding.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/phase.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/reference.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/sam_view.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/sample.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/samtools.pysam.c -o build/temp.linux-x86_64-3.10/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/stats.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcsamtools.o build/temp.linux-x86_64-3.10/samtools/amplicon_stats.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_consensus.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_samples.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-3.10/samtools/consensus_pileup.c.pysam.o build/temp.linux-x86_64-3.10/samtools/coverage.c.pysam.o build/temp.linux-x86_64-3.10/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-3.10/samtools/dict.c.pysam.o build/temp.linux-x86_64-3.10/samtools/faidx.c.pysam.o build/temp.linux-x86_64-3.10/samtools/lz4/lz4.o build/temp.linux-x86_64-3.10/samtools/padding.c.pysam.o build/temp.linux-x86_64-3.10/samtools/phase.c.pysam.o build/temp.linux-x86_64-3.10/samtools/reference.c.pysam.o build/temp.linux-x86_64-3.10/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-3.10/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-3.10/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-3.10/samtools/sample.c.pysam.o build/temp.linux-x86_64-3.10/samtools/samtools.pysam.o build/temp.linux-x86_64-3.10/samtools/stats.c.pysam.o build/temp.linux-x86_64-3.10/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-3.10/samtools/tmp_file.c.pysam.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamtools.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-x86_64-3.10/bcftools x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/HMM.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/abuf.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/bcftools.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/bin.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/ccall.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/cols.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/consensus.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/convert.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/csq.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/dist.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/em.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/extsort.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/filter.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/hclust.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/kmin.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/main.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/mcall.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/prob1.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/regidx.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/reheader.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/tabix.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-x86_64-3.10/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:751:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 751 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:30, from /usr/include/htslib/hts.h:37, from /usr/include/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:556:14: note: in a call to allocation function ‘calloc’ declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c bcftools/version.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libcbcftools.c -o build/temp.linux-x86_64-3.10/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/abuf.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/bcftools.pysam.o build/temp.linux-x86_64-3.10/bcftools/bin.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/cols.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/convert.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/csq.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/dist.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/em.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/extsort.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/filter.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/main.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/reheader.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/str_finder.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfhead.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfroh.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfstats.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/version.c.pysam.o build/temp.linux-x86_64-3.10/pysam/libcbcftools.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcftools.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 751 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^ /usr/include/stdlib.h:556:14: note: in a call to allocation function ‘calloc’ declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^ building 'pysam.libcutils' extension x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libcutils.c -o build/temp.linux-x86_64-3.10/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/pysam_util.c -o build/temp.linux-x86_64-3.10/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcutils.o build/temp.linux-x86_64-3.10/pysam/pysam_util.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcsamtools.cpython-310-x86_64-linux-gnu -lcbcftools.cpython-310-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcutils.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libcalignmentfile.c -o build/temp.linux-x86_64-3.10/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcalignmentfile.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignmentfile.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libcsamfile.c -o build/temp.linux-x86_64-3.10/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcsamfile.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamfile.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libcalignedsegment.c -o build/temp.linux-x86_64-3.10/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcalignedsegment.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignedsegment.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libctabix.c -o build/temp.linux-x86_64-3.10/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libctabix.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libctabix.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libcfaidx.c -o build/temp.linux-x86_64-3.10/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcfaidx.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcfaidx.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libcbcf.c -o build/temp.linux-x86_64-3.10/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcbcf.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcf.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libcbgzf.c -o build/temp.linux-x86_64-3.10/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcbgzf.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcbgzf.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-3.10/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libctabixproxies.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libctabixproxies.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.10 -c pysam/libcvcf.c -o build/temp.linux-x86_64-3.10/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.constprop.0’: pysam/libcvcf.c:25229:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 25229 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:19949:10: note: ‘__pyx_v_qual’ was declared here 19949 | double __pyx_v_qual; | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcvcf.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -L/<>/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcvcf.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test make[1]: Entering directory '/<>' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/<>/tests/pysam_data' samtools faidx ex1.fa samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz 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 --no-PG -h ex1.bam | gzip > ex2.sam.gz gunzip < ex2.sam.gz > ex2.sam samtools view --no-PG -bo ex2.bam ex2.sam samtools index ex2.bam samtools calmd --no-PG --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 --no-PG -bo with_md.bam with_md.sam [W::bam_hdr_read] EOF marker is absent. The input is probably truncated samtools index with_md.bam samtools view --no-PG -bu -o uncompressed.bam ex2.sam samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam samtools view --no-PG -bo MM-double.bam MM-double.sam samtools view --no-PG -bo MM-multi.bam MM-multi.sam samtools view --no-PG -bo MM-orient.bam MM-orient.sam samtools view --no-PG -bo ex10.bam ex10.sam samtools view --no-PG -bo ex3.bam ex3.sam samtools view --no-PG -bo ex4.bam ex4.sam samtools view --no-PG -bo ex5.bam ex5.sam samtools view --no-PG -bo ex6.bam ex6.sam samtools view --no-PG -bo ex8.bam ex8.sam samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam samtools view --no-PG -bo example_btag.bam example_btag.sam samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam touch tmp.list samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam rm -f tmp.list samtools view --no-PG -bo issue100.bam issue100.sam samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam samtools view --no-PG -bo softclip.bam softclip.sam samtools view --no-PG -bo tag_bug.bam tag_bug.sam samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam samtools view --no-PG -bo test_query_position.bam test_query_position.sam samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam samtools index MM-chebi.bam samtools index MM-double.bam samtools index MM-multi.bam samtools index MM-orient.bam samtools index ex10.bam samtools index ex3.bam samtools index ex4.bam samtools index ex5.bam samtools index ex6.bam samtools index ex8.bam samtools index ex9_fail.bam samtools index ex9_nofail.bam samtools index ex_spliced.bam samtools index example_aligned_pairs.bam samtools index example_btag.bam samtools index example_dash_in_chr.bam samtools index example_empty_header.bam samtools index example_empty_with_header.bam samtools index example_reverse_complement.bam samtools index example_unmapped_reads_no_sq.bam samtools index issue100.bam samtools index rg_with_tab.bam samtools index softclip.bam samtools index tag_bug.bam samtools index test_mapped_unmapped.bam samtools index test_query_position.bam samtools index test_unaligned.bam samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam 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 dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 1+0 records in 1+0 records out 122292 bytes (122 kB, 119 KiB) copied, 0.000228517 s, 535 MB/s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam grep "^@" ex2.sam | samtools view --no-PG -bo 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 touch all.stamp rm with_md.sam make[2]: Leaving directory '/<>/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make all make[2]: Entering directory '/<>/tests/cbcf_data' 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 < 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 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_vcf43.vcf > example_vcf43.vcf.gz tabix -p vcf example_vcf43.vcf.gz # create tbi index bcftools index example_vcf43.vcf.gz # create csi index bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index bcftools index example_vcf43_with_utf8.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 < 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 < 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 bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf bcftools index example_vcf40.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 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_vcf43.vcf.gz -o example_vcf43.bcf bcftools index example_vcf43.bcf bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf bcftools index example_vcf43_with_utf8.bcf bcftools view -O b gnomad.vcf.gz -o gnomad.bcf bcftools index gnomad.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 missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf touch all.stamp make[2]: Leaving directory '/<>/tests/cbcf_data' dh_auto_test I: pybuild base:240: cd /<>/.pybuild/cpython3_3.10_pysam/build; python3.10 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.10.8, pytest-7.1.2, pluggy-1.0.0+repack -- /usr/bin/python3.10 cachedir: .pytest_cache rootdir: /<>, configfile: setup.cfg collecting ... collected 949 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::testUpdateQual 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_padding_with_seq 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::TestBaseModifications::testChebi PASSED tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED tests/AlignedSegment_test.py::TestBaseModifications::testOrient 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp___enter___pdrs8dqmnegative_integers.bam' 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_r0bcq71m' /<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_r0bcq71m PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_s6ayitht' /<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_s6ayitht PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ogextme5 PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_sylyvoz8' /<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_sylyvoz8 PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 [E::cram_index_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_wkt8aj7q' /<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_wkt8aj7q PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ixyaxp2p 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::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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_eyzh59s9tmp_ex2.bam' 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" : No such file or directory 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_ch5tt94btmp_single.bam' [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_hbaxle_wtmp_multi.bam' 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" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 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::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/pysam_data/0example_no_seq_in_header.bam' PASSED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/pysam_data/0example_no_seq_in_header_null_bytes.bam' 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::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/pysam_data/ex2_truncated.bam' [E::bgzf_read_block] Failed to read BGZF block data at offset 105180 expected 17578 bytes; hread returned 17094 [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/pysam_data/ex2_corrupt.bam' 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" : No such file or directory PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM 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::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_5pw5i59_tmp_largecigar.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" : No such file or directory PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory 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::testAllelesVariantTypes 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_13zfq3m4.bcf' PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [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.) [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::TestUnicode::test_record_with_unicode PASSED tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED tests/VariantRecord_test.py::test_set_sample_alleles 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/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error 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 (skipping us...) tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag 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 (skipping usage...) 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::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_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_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_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_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_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_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::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_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_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_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_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_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_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_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_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_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_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_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_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_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::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::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] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse_info] 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_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] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 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_24::testConnecting [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: #CHROM POS ID REF ALT QUAL FILTER INFO PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 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' at 20:676148 is not defined in the header, assuming Type=String 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] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 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_5::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G 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_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] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 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' at 20:249843 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting [W::bcf_hrec_check] Invalid tag name: "1000g" [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::bcf_hrec_check] Invalid tag name: "1000g" [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] 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_23::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] 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_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' at 20:676148 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' at 20:439104 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] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 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_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_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' at 20:669442 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_20::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 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] INFO 'sumGLbyD' 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' at 20:249843 is not defined in the header, assuming Type=String 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] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 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::TestBED::testAssignmentToTargetList PASSED tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList 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::testAssignmentToTargetList 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::testAssignmentToTargetList 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/python3/dist-packages/pyximport/pyximport.py:51 /usr/lib/python3/dist-packages/pyximport/pyximport.py:51: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses import imp tests/_compile_test.pyxbld:3 /<>/.pybuild/cpython3_3.10_pysam/build/tests/_compile_test.pyxbld:3: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.extension import Extension ../../../../../../usr/lib/python3.10/distutils/command/build_ext.py:13 /usr/lib/python3.10/distutils/command/build_ext.py:13: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead from distutils.sysconfig import customize_compiler, get_python_version ../../../../../../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: /<>/.pybuild/cpython3_3.10_pysam/build/tests/_compile_test.pyx tree = Parsing.p_module(s, pxd, full_module_name) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================= 939 passed, 10 skipped, 4 warnings in 25.59s ================= make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /<>/debian/python3-pysam /<>/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils import log # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py copying pysam/config.py -> /<>/.pybuild/cpython3_3.10_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) copying samtools/samtools_config_vars.h -> /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools 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) creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension running install_lib creating /<>/debian/python3-pysam creating /<>/debian/python3-pysam/usr creating /<>/debian/python3-pysam/usr/lib creating /<>/debian/python3-pysam/usr/lib/python3.10 creating /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages creating /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcvcf.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignedsegment.pxd -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcftools.pxd -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignmentfile.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcftools.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam creating /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/__init__.py -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include creating /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/regidx.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/HMM.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/str_finder.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/bcftools.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/utlist.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/kmin.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/bin.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/variantkey.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/hclust.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/rbuf.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/abuf.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/gvcf.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/convert.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/mw.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/kheap.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/config.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/prob1.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/filter.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/bam_sample.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/vcmp.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/ploidy.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/call.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/dbuf.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/cols.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/hex.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/dist.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/extsort.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools creating /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/consensus_pileup.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/samtools.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/config.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/splaysort.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/sam_opts.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/bam_ampliconclip.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/samtools_config_vars.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/bam.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/tmp_file.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/bedidx.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/stats_isize.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/sample.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/pysam_stream.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libctabixproxies.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcfaidx.pxd -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libctabix.pxd -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/pysam_util.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcfaidx.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/Pileup.py -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcf.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/bcftools.py -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcutils.pxd -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcbgzf.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignmentfile.pxd -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/py.typed -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcftools.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libctabix.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamtools.pxd -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/cbcftools_util.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamfile.pxd -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libchtslib.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libchtslib.pxd -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcf.pxd -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/__init__.py -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/htslib_util.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libctabixproxies.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamfile.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/version.py -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcvcf.pxd -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignmentfile.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam creating /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/__pycache__/config.cpython-310.pyc -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/__pycache__/version.cpython-310.pyc -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/__pycache__/samtools.cpython-310.pyc -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/__pycache__/bcftools.cpython-310.pyc -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/__pycache__/utils.cpython-310.pyc -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/__pycache__/__init__.cpython-310.pyc -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/__pycache__/Pileup.cpython-310.pyc -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamtools.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libchtslib.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/csamtools_util.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamtools.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libctabix.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/utils.py -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignedsegment.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcfaidx.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/samtools.py -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcbgzf.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamfile.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcutils.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcvcf.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/config.py -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/version.h -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libctabixproxies.pxd -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignedsegment.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcutils.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/version.pyi -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /<>/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcf.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam byte-compiling /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/Pileup.py to Pileup.cpython-310.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/bcftools.py to bcftools.cpython-310.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/version.py to version.cpython-310.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/utils.py to utils.cpython-310.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/samtools.py to samtools.cpython-310.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/config.py to config.cpython-310.pyc running install_egg_info running egg_info creating pysam.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 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' warning: no files found matching 'win32/*.[ch]' no previously-included directories found matching 'tests/' warning: no files found matching 'htslib/LICENSE' warning: no files found matching 'htslib/README' warning: no files found matching '*.[ch]' under directory 'htslib' warning: no previously-included files found matching 'htslib/*config*.h' warning: no files found matching 'htslib/configure.ac' warning: no files found matching 'htslib/m4/*.m4' warning: no files found matching 'htslib/*.in' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/version.sh' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/*.mk' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam-0.20.0.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/<>' cd tests/pysam_data && /usr/bin/make clean make[2]: Entering directory '/<>/tests/pysam_data' rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz make[2]: Leaving directory '/<>/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[2]: Entering directory '/<>/tests/cbcf_data' rm -f all.stamp *.gz *.tbi *.csi *.bcf make[2]: Leaving directory '/<>/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete 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 '/<>' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcvcf.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 4140fe2ca80a18e824fd665acd02c2a2ea988122 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcalignmentfile.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 60e11a6b4fed6a53bd3ff7b429c56ddbffa49497 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 5e3ee5193d9ddf12400e4699c8e2f395305ff8cb debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbgzf.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 296c5b11b63ed516eb9fd3e3fe89e1096fd0355c debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcftools.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 c278fa4d38638c8bf93b2ed9dfb2d982cbbbc797 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libchtslib.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 fc82b04fec6143d775449e650f5dfbb7aafa5768 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 a86e4608b4fcfb9b6d9f9ff7e9b1de9846c76cab debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcsamtools.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 457438de0a2b0f9a43093b6fa288509c1280983b debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libctabix.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 e8e0e32d34bc422efb77990d77fa5b0662fabd7e debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcalignedsegment.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 d2fc6c1a010c9b098d85d616e05f83aa7eda67a1 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 e3688824e85699371afc526e549ada092977c1f6 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcutils.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 cfa77b12fcc62c7abded041e7972dce23ab80576 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcf.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 ef1e5d7f341b8baf6f0b96d7c30a10a02da54603 dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing python-pysam-tests (in debian/python-pysam-tests); do_strip: , oemstrip: 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: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python-pysam-tests/DEBIAN/control, package python-pysam-tests, directory debian/python-pysam-tests INFO: pkgstripfiles: waiting for lock (python-pysam-tests) ... pkgstripfiles: processing control file: debian/python3-pysam/DEBIAN/control, package python3-pysam, directory debian/python3-pysam 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. 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' in '../python3-pysam_0.20.0+ds-1_amd64.deb'. dpkg-deb: building package 'python3-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-pysam/python3-pysam-dbgsym_0.20.0+ds-1_amd64.deb'. pkgstripfiles: Truncating usr/share/doc/python-pysam-tests/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pysam-tests ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-pysam-tests' in '../python-pysam-tests_0.20.0+ds-1_all.deb'. Renaming python3-pysam-dbgsym_0.20.0+ds-1_amd64.deb to python3-pysam-dbgsym_0.20.0+ds-1_amd64.ddeb dpkg-genbuildinfo --build=binary -O../python-pysam_0.20.0+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../python-pysam_0.20.0+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-11-30T05:32:26Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-pysam_0.20.0+ds-1_amd64.changes: --------------------------------------- Format: 1.8 Date: Tue, 29 Nov 2022 21:55:48 +0100 Source: python-pysam Binary: python-pysam-tests python3-pysam Built-For-Profiles: noudeb Architecture: all amd64 Version: 0.20.0+ds-1 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: python-pysam-tests - 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 (0.20.0+ds-1) unstable; urgency=medium . * New upstream version * Update lintian override info format in d/python-pysam.lintian-overrides on line 4. * skip_test_remote.patch: refresh. * test-truncated-bam.patch: delete; applied upstream. * d/control: make build only depend on python3-dev. * d/control: disable autopkgtest-pkg-python due to missing python3.11 support; classical autopkgtest is still active though. Checksums-Sha1: 5aee302ea63ae6dfff52bd0867a21a46d3928d46 1428544 python-pysam-tests_0.20.0+ds-1_all.deb 0c9d534c468cc5771773dd1d9cf97698405f2e82 8129 python-pysam_0.20.0+ds-1_amd64.buildinfo cf69b98d9a73bf17af5fb8f20058110b25ca3ca9 6928422 python3-pysam-dbgsym_0.20.0+ds-1_amd64.ddeb bca9ffb4f6ddd108094346a3e570f91589bec80e 1783040 python3-pysam_0.20.0+ds-1_amd64.deb Checksums-Sha256: 7bfa1b176e48ed7e8e769967ea4ff3252134c6b2e4d989d292a165593b0bc42a 1428544 python-pysam-tests_0.20.0+ds-1_all.deb 1ad051049ebc80b9ea75a03558428d5bae3219faddb19009251f44fb669f32f4 8129 python-pysam_0.20.0+ds-1_amd64.buildinfo b28e4744c26a63dac49b0af81fd3f602bcd04e1c4aaeead360c3adc9289f3aca 6928422 python3-pysam-dbgsym_0.20.0+ds-1_amd64.ddeb 6e4f3be53ea5b539350298a5b88fae5be2202cd8d6ee8b91027d46972d5d790f 1783040 python3-pysam_0.20.0+ds-1_amd64.deb Files: dd48df79e1de03cdaefefd208e110a99 1428544 python optional python-pysam-tests_0.20.0+ds-1_all.deb b95ecb3b3f7220631841f0313a70d5a7 8129 python optional python-pysam_0.20.0+ds-1_amd64.buildinfo b97bf70079f8d11df7c50a9e6435c18c 6928422 debug optional python3-pysam-dbgsym_0.20.0+ds-1_amd64.ddeb 04134b9ae5a3919a0691c6164bcc52ff 1783040 python optional python3-pysam_0.20.0+ds-1_amd64.deb /<>/python-pysam_0.20.0+ds-1_amd64.changes.new could not be renamed to /<>/python-pysam_0.20.0+ds-1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: python-pysam Binary: python-pysam-tests python3-pysam python3-pysam-dbgsym Architecture: all amd64 Version: 0.20.0+ds-1 Checksums-Md5: dd48df79e1de03cdaefefd208e110a99 1428544 python-pysam-tests_0.20.0+ds-1_all.deb b97bf70079f8d11df7c50a9e6435c18c 6928422 python3-pysam-dbgsym_0.20.0+ds-1_amd64.ddeb 04134b9ae5a3919a0691c6164bcc52ff 1783040 python3-pysam_0.20.0+ds-1_amd64.deb Checksums-Sha1: 5aee302ea63ae6dfff52bd0867a21a46d3928d46 1428544 python-pysam-tests_0.20.0+ds-1_all.deb cf69b98d9a73bf17af5fb8f20058110b25ca3ca9 6928422 python3-pysam-dbgsym_0.20.0+ds-1_amd64.ddeb bca9ffb4f6ddd108094346a3e570f91589bec80e 1783040 python3-pysam_0.20.0+ds-1_amd64.deb Checksums-Sha256: 7bfa1b176e48ed7e8e769967ea4ff3252134c6b2e4d989d292a165593b0bc42a 1428544 python-pysam-tests_0.20.0+ds-1_all.deb b28e4744c26a63dac49b0af81fd3f602bcd04e1c4aaeead360c3adc9289f3aca 6928422 python3-pysam-dbgsym_0.20.0+ds-1_amd64.ddeb 6e4f3be53ea5b539350298a5b88fae5be2202cd8d6ee8b91027d46972d5d790f 1783040 python3-pysam_0.20.0+ds-1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Wed, 30 Nov 2022 05:32:26 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-10), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2-1ubuntu2), bcftools (= 1.16-1), binutils (= 2.39-8ubuntu2), binutils-common (= 2.39-8ubuntu2), binutils-x86-64-linux-gnu (= 2.39-8ubuntu2), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:12.2.0-1ubuntu1), cpp-12 (= 12.2.0-9ubuntu1), cython3 (= 0.29.32-1ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-8ubuntu1), debconf (= 1.5.80), debhelper (= 13.10.1ubuntu1), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-exec (= 0.27), dh-python (= 5.20221122), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-1), dpkg (= 1.21.9ubuntu1), dpkg-dev (= 1.21.9ubuntu1), dwz (= 0.14+20220924-2), file (= 1:5.41-4), findutils (= 4.9.0-3ubuntu1), g++ (= 4:12.2.0-1ubuntu1), g++-12 (= 12.2.0-9ubuntu1), gcc (= 4:12.2.0-1ubuntu1), gcc-12 (= 12.2.0-9ubuntu1), gcc-12-base (= 12.2.0-9ubuntu1), gettext (= 0.21-10), gettext-base (= 0.21-10), grep (= 3.8-3), groff-base (= 1.22.4-9), gzip (= 1.12-1ubuntu1), hostname (= 3.23ubuntu2), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 12.2.0-9ubuntu1), libatomic1 (= 12.2.0-9ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1ubuntu2), libaudit1 (= 1:3.0.7-1ubuntu2), libbinutils (= 2.39-8ubuntu2), libblkid1 (= 2.38-4ubuntu1), libbrotli1 (= 1.0.9-2build7), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.36-0ubuntu4), libc-dev-bin (= 2.36-0ubuntu4), libc6 (= 2.36-0ubuntu4), libc6-dev (= 2.36-0ubuntu4), libcap-ng0 (= 0.8.3-1build1), libcap2 (= 1:2.44-1build3), libcc1-0 (= 12.2.0-9ubuntu1), libcom-err2 (= 1.46.6~rc1-1ubuntu1), libcrypt-dev (= 1:4.4.33-1), libcrypt1 (= 1:4.4.33-1), libctf-nobfd0 (= 2.39-8ubuntu2), libctf0 (= 2.39-8ubuntu2), libcurl3-gnutls (= 7.86.0-2), libcurl4-gnutls-dev (= 7.86.0-2), libdb5.3 (= 5.3.28+dfsg1-0.10), libdebconfclient0 (= 0.264ubuntu1), libdebhelper-perl (= 13.10.1ubuntu1), libdeflate-dev (= 1.14-1), libdeflate0 (= 1.14-1), libdpkg-perl (= 1.21.9ubuntu1), libdw1 (= 0.188-1), libelf1 (= 0.188-1), libexpat1 (= 2.5.0-1), libexpat1-dev (= 2.5.0-1), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.0-1), libgcc-12-dev (= 12.2.0-9ubuntu1), libgcc-s1 (= 12.2.0-9ubuntu1), libgcrypt20 (= 1.10.1-2ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.2.1+dfsg1-1ubuntu2), libgnutls30 (= 3.7.7-2ubuntu2), libgomp1 (= 12.2.0-9ubuntu1), libgpg-error0 (= 1.46-1), libgprofng0 (= 2.39-8ubuntu2), libgssapi-krb5-2 (= 1.20.1-1), libhogweed6 (= 3.8.1-2), libhts-dev (= 1.16+ds-3), libhts3 (= 1.16+ds-3), libhtscodecs2 (= 1.3.0-4), libicu71 (= 71.1-3ubuntu1), libidn2-0 (= 2.3.3-1build1), libisl23 (= 0.25-1), libitm1 (= 12.2.0-9ubuntu1), libjs-jquery (= 3.6.0+dfsg+~3.5.13-1), libjs-sphinxdoc (= 4.5.0-4), libjs-underscore (= 1.13.4~dfsg+~1.11.4-2), libk5crypto3 (= 1.20.1-1), libkeyutils1 (= 1.6.3-1), libkrb5-3 (= 1.20.1-1), libkrb5support0 (= 1.20.1-1), libldap-2.5-0 (= 2.5.13+dfsg-1ubuntu1), liblsan0 (= 12.2.0-9ubuntu1), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.2.8-0.0), liblzma5 (= 5.2.8-0.0), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmount1 (= 2.38-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpdec3 (= 2.5.1-2build2), libmpfr6 (= 4.1.0-3build3), libncurses6 (= 6.3+20220423-2), libncursesw6 (= 6.3+20220423-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.50.0-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libp11-kit0 (= 0.24.1-1ubuntu2), libpam-modules (= 1.5.2-5ubuntu1), libpam-modules-bin (= 1.5.2-5ubuntu1), libpam-runtime (= 1.5.2-5ubuntu1), libpam0g (= 1.5.2-5ubuntu1), libpcre2-8-0 (= 10.40-1ubuntu1), libperl5.36 (= 5.36.0-4ubuntu2), libpipeline1 (= 1.5.7-1), libpsl5 (= 0.21.0-1.2build2), libpython3-dev (= 3.10.6-1ubuntu1), libpython3-stdlib (= 3.10.6-1ubuntu1), libpython3.10 (= 3.10.8-3), libpython3.10-dev (= 3.10.8-3), libpython3.10-minimal (= 3.10.8-3), libpython3.10-stdlib (= 3.10.8-3), libquadmath0 (= 12.2.0-9ubuntu1), 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Packaging Team Installed-Size: 2772 Enhances: python3-pysam Section: python Priority: optional Multi-Arch: foreign Homepage: https://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (test data) 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. . 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sequence alignment and mapping format (Python 3) Pysam is a Python module for reading and manipulating Samfiles. 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+------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 156860 Build-Time: 232 Distribution: lunar-proposed Host Architecture: amd64 Install-Time: 12 Job: python-pysam_0.20.0+ds-1.dsc Machine Architecture: amd64 Package: python-pysam Package-Time: 244 Source-Version: 0.20.0+ds-1 Space: 156860 Status: successful Version: 0.20.0+ds-1 -------------------------------------------------------------------------------- Finished at 2022-11-30T05:32:26Z Build needed 00:04:04, 156860k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24884798 Scanning for processes to kill in build PACKAGEBUILD-24884798