https://launchpad.net/ubuntu/+source/bcftools/1.7-2/+build/14825711 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-s390x-008 4.4.0-122-generic #146-Ubuntu SMP Mon Apr 23 15:33:03 UTC 2018 s390x Buildd toolchain package versions: launchpad-buildd_161 python-lpbuildd_161 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 4 May 16:04:29 ntpdate[1762]: adjust time server 10.211.37.1 offset -0.012119 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=cosmic --arch=s390x PACKAGEBUILD-14825711 /home/buildd/filecache-default/17124f3eec304530bbb077109f97da7d4ad52147 Creating target for build PACKAGEBUILD-14825711 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=cosmic --arch=s390x PACKAGEBUILD-14825711 Starting target for build PACKAGEBUILD-14825711 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=cosmic --arch=s390x PACKAGEBUILD-14825711 'deb http://ftpmaster.internal/ubuntu cosmic main universe' Overriding sources.list in build-PACKAGEBUILD-14825711 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=cosmic --arch=s390x PACKAGEBUILD-14825711 Updating target for build PACKAGEBUILD-14825711 Get:1 http://ftpmaster.internal/ubuntu cosmic InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic/main s390x Packages [942 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main Translation-en [516 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/universe s390x Packages [8170 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/universe Translation-en [4941 kB] Fetched 14.8 MB in 3s (5231 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libncurses6 libncursesw6 libtinfo6 The following packages will be upgraded: base-files bash binutils binutils-common binutils-s390x-linux-gnu cpp-7 g++-7 gcc-7 gcc-7-base gcc-8-base libasan4 libatomic1 libbinutils libcc1-0 libgcc-7-dev libgcc1 libgomp1 libitm1 libncurses5 libncursesw5 libprocps6 libreadline7 libstdc++-7-dev libstdc++6 libtinfo5 libubsan0 ncurses-base ncurses-bin procps readline-common 30 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 24.2 MB of archives. After this operation, 1281 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu cosmic/main s390x base-files s390x 10.1ubuntu3 [58.0 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic/main s390x libtinfo6 s390x 6.1+20180210-2ubuntu2 [80.5 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main s390x bash s390x 4.4.18-2ubuntu2 [583 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main s390x ncurses-bin s390x 6.1+20180210-2ubuntu2 [159 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main s390x ncurses-base all 6.1+20180210-2ubuntu2 [17.8 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main s390x libgomp1 s390x 8.1.0-1ubuntu2 [69.8 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main s390x libitm1 s390x 8.1.0-1ubuntu2 [26.9 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main s390x gcc-8-base s390x 8.1.0-1ubuntu2 [18.1 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main s390x libstdc++6 s390x 8.1.0-1ubuntu2 [398 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main s390x libcc1-0 s390x 8.1.0-1ubuntu2 [37.3 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic/main s390x libatomic1 s390x 8.1.0-1ubuntu2 [8428 B] Get:12 http://ftpmaster.internal/ubuntu cosmic/main s390x libgcc1 s390x 1:8.1.0-1ubuntu2 [25.1 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic/main s390x libncurses5 s390x 6.1+20180210-2ubuntu2 [89.0 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main s390x libtinfo5 s390x 6.1+20180210-2ubuntu2 [76.2 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main s390x libncursesw5 s390x 6.1+20180210-2ubuntu2 [108 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main s390x libprocps6 s390x 2:3.3.12-3ubuntu2 [30.1 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main s390x libncurses6 s390x 6.1+20180210-2ubuntu2 [94.3 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main s390x libncursesw6 s390x 6.1+20180210-2ubuntu2 [120 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main s390x procps s390x 2:3.3.12-3ubuntu2 [215 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic/main s390x readline-common all 7.0-4 [52.9 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main s390x libreadline7 s390x 7.0-4 [117 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main s390x libbinutils s390x 2.30-17ubuntu1 [305 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main s390x binutils-common s390x 2.30-17ubuntu1 [193 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main s390x binutils s390x 2.30-17ubuntu1 [3324 B] Get:25 http://ftpmaster.internal/ubuntu cosmic/main s390x binutils-s390x-linux-gnu s390x 2.30-17ubuntu1 [1722 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main s390x libasan4 s390x 7.3.0-17ubuntu1 [318 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic/main s390x libubsan0 s390x 7.3.0-17ubuntu1 [120 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main s390x g++-7 s390x 7.3.0-17ubuntu1 [5989 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main s390x gcc-7 s390x 7.3.0-17ubuntu1 [5886 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main s390x libstdc++-7-dev s390x 7.3.0-17ubuntu1 [1454 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main s390x libgcc-7-dev s390x 7.3.0-17ubuntu1 [641 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic/main s390x cpp-7 s390x 7.3.0-17ubuntu1 [5186 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main s390x gcc-7-base s390x 7.3.0-17ubuntu1 [18.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 24.2 MB in 0s (52.0 MB/s) (Reading database ... 12382 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu3_s390x.deb ... Unpacking base-files (10.1ubuntu3) over (10.1ubuntu2) ... Setting up base-files (10.1ubuntu3) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Selecting previously unselected package libtinfo6:s390x. (Reading database ... 12382 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20180210-2ubuntu2_s390x.deb ... Unpacking libtinfo6:s390x (6.1+20180210-2ubuntu2) ... Setting up libtinfo6:s390x (6.1+20180210-2ubuntu2) ... (Reading database ... 12391 files and directories currently installed.) Preparing to unpack .../bash_4.4.18-2ubuntu2_s390x.deb ... Unpacking bash (4.4.18-2ubuntu2) over (4.4.18-2ubuntu1) ... Setting up bash (4.4.18-2ubuntu2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12391 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.1+20180210-2ubuntu2_s390x.deb ... Unpacking ncurses-bin (6.1+20180210-2ubuntu2) over (6.1-1ubuntu1) ... Setting up ncurses-bin (6.1+20180210-2ubuntu2) ... (Reading database ... 12391 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.1+20180210-2ubuntu2_all.deb ... Unpacking ncurses-base (6.1+20180210-2ubuntu2) over (6.1-1ubuntu1) ... Setting up ncurses-base (6.1+20180210-2ubuntu2) ... (Reading database ... 12391 files and directories currently installed.) Preparing to unpack .../libgomp1_8.1.0-1ubuntu2_s390x.deb ... Unpacking libgomp1:s390x (8.1.0-1ubuntu2) over (8-20180414-1ubuntu2) ... Preparing to unpack .../libitm1_8.1.0-1ubuntu2_s390x.deb ... Unpacking libitm1:s390x (8.1.0-1ubuntu2) over (8-20180414-1ubuntu2) ... Preparing to unpack .../gcc-8-base_8.1.0-1ubuntu2_s390x.deb ... Unpacking gcc-8-base:s390x (8.1.0-1ubuntu2) over (8-20180414-1ubuntu2) ... Setting up gcc-8-base:s390x (8.1.0-1ubuntu2) ... (Reading database ... 12390 files and directories currently installed.) Preparing to unpack .../libstdc++6_8.1.0-1ubuntu2_s390x.deb ... Unpacking libstdc++6:s390x (8.1.0-1ubuntu2) over (8-20180414-1ubuntu2) ... Setting up libstdc++6:s390x (8.1.0-1ubuntu2) ... (Reading database ... 12390 files and directories currently installed.) Preparing to unpack .../libcc1-0_8.1.0-1ubuntu2_s390x.deb ... Unpacking libcc1-0:s390x (8.1.0-1ubuntu2) over (8-20180414-1ubuntu2) ... Preparing to unpack .../libatomic1_8.1.0-1ubuntu2_s390x.deb ... Unpacking libatomic1:s390x (8.1.0-1ubuntu2) over (8-20180414-1ubuntu2) ... Preparing to unpack .../libgcc1_1%3a8.1.0-1ubuntu2_s390x.deb ... Unpacking libgcc1:s390x (1:8.1.0-1ubuntu2) over (1:8-20180414-1ubuntu2) ... Setting up libgcc1:s390x (1:8.1.0-1ubuntu2) ... (Reading database ... 12390 files and directories currently installed.) Preparing to unpack .../libncurses5_6.1+20180210-2ubuntu2_s390x.deb ... Unpacking libncurses5:s390x (6.1+20180210-2ubuntu2) over (6.1-1ubuntu1) ... Preparing to unpack .../libtinfo5_6.1+20180210-2ubuntu2_s390x.deb ... Unpacking libtinfo5:s390x (6.1+20180210-2ubuntu2) over (6.1-1ubuntu1) ... Setting up libtinfo5:s390x (6.1+20180210-2ubuntu2) ... (Reading database ... 12388 files and directories currently installed.) Preparing to unpack .../libncursesw5_6.1+20180210-2ubuntu2_s390x.deb ... Unpacking libncursesw5:s390x (6.1+20180210-2ubuntu2) over (6.1-1ubuntu1) ... Setting up libncursesw5:s390x (6.1+20180210-2ubuntu2) ... (Reading database ... 12388 files and directories currently installed.) Preparing to unpack .../00-libprocps6_2%3a3.3.12-3ubuntu2_s390x.deb ... Unpacking libprocps6:s390x (2:3.3.12-3ubuntu2) over (2:3.3.12-3ubuntu1) ... Selecting previously unselected package libncurses6:s390x. Preparing to unpack .../01-libncurses6_6.1+20180210-2ubuntu2_s390x.deb ... Unpacking libncurses6:s390x (6.1+20180210-2ubuntu2) ... Selecting previously unselected package libncursesw6:s390x. Preparing to unpack .../02-libncursesw6_6.1+20180210-2ubuntu2_s390x.deb ... Unpacking libncursesw6:s390x (6.1+20180210-2ubuntu2) ... Preparing to unpack .../03-procps_2%3a3.3.12-3ubuntu2_s390x.deb ... Unpacking procps (2:3.3.12-3ubuntu2) over (2:3.3.12-3ubuntu1) ... Preparing to unpack .../04-readline-common_7.0-4_all.deb ... Unpacking readline-common (7.0-4) over (7.0-3) ... Preparing to unpack .../05-libreadline7_7.0-4_s390x.deb ... Unpacking libreadline7:s390x (7.0-4) over (7.0-3) ... Preparing to unpack .../06-libbinutils_2.30-17ubuntu1_s390x.deb ... Unpacking libbinutils:s390x (2.30-17ubuntu1) over (2.30-15ubuntu1) ... Preparing to unpack .../07-binutils-common_2.30-17ubuntu1_s390x.deb ... Unpacking binutils-common:s390x (2.30-17ubuntu1) over (2.30-15ubuntu1) ... Preparing to unpack .../08-binutils_2.30-17ubuntu1_s390x.deb ... Unpacking binutils (2.30-17ubuntu1) over (2.30-15ubuntu1) ... Preparing to unpack .../09-binutils-s390x-linux-gnu_2.30-17ubuntu1_s390x.deb ... Unpacking binutils-s390x-linux-gnu (2.30-17ubuntu1) over (2.30-15ubuntu1) ... Preparing to unpack .../10-libasan4_7.3.0-17ubuntu1_s390x.deb ... Unpacking libasan4:s390x (7.3.0-17ubuntu1) over (7.3.0-16ubuntu3) ... Preparing to unpack .../11-libubsan0_7.3.0-17ubuntu1_s390x.deb ... Unpacking libubsan0:s390x (7.3.0-17ubuntu1) over (7.3.0-16ubuntu3) ... Preparing to unpack .../12-g++-7_7.3.0-17ubuntu1_s390x.deb ... Unpacking g++-7 (7.3.0-17ubuntu1) over (7.3.0-16ubuntu3) ... Preparing to unpack .../13-gcc-7_7.3.0-17ubuntu1_s390x.deb ... Unpacking gcc-7 (7.3.0-17ubuntu1) over (7.3.0-16ubuntu3) ... Preparing to unpack .../14-libstdc++-7-dev_7.3.0-17ubuntu1_s390x.deb ... Unpacking libstdc++-7-dev:s390x (7.3.0-17ubuntu1) over (7.3.0-16ubuntu3) ... Preparing to unpack .../15-libgcc-7-dev_7.3.0-17ubuntu1_s390x.deb ... Unpacking libgcc-7-dev:s390x (7.3.0-17ubuntu1) over (7.3.0-16ubuntu3) ... Preparing to unpack .../16-cpp-7_7.3.0-17ubuntu1_s390x.deb ... Unpacking cpp-7 (7.3.0-17ubuntu1) over (7.3.0-16ubuntu3) ... Preparing to unpack .../17-gcc-7-base_7.3.0-17ubuntu1_s390x.deb ... Unpacking gcc-7-base:s390x (7.3.0-17ubuntu1) over (7.3.0-16ubuntu3) ... Setting up libncurses5:s390x (6.1+20180210-2ubuntu2) ... Setting up libgomp1:s390x (8.1.0-1ubuntu2) ... Setting up libatomic1:s390x (8.1.0-1ubuntu2) ... Setting up readline-common (7.0-4) ... Setting up libcc1-0:s390x (8.1.0-1ubuntu2) ... Setting up libreadline7:s390x (7.0-4) ... Setting up libncursesw6:s390x (6.1+20180210-2ubuntu2) ... Setting up libprocps6:s390x (2:3.3.12-3ubuntu2) ... Setting up gcc-7-base:s390x (7.3.0-17ubuntu1) ... Setting up binutils-common:s390x (2.30-17ubuntu1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up libncurses6:s390x (6.1+20180210-2ubuntu2) ... Setting up libitm1:s390x (8.1.0-1ubuntu2) ... Setting up libasan4:s390x (7.3.0-17ubuntu1) ... Setting up libbinutils:s390x (2.30-17ubuntu1) ... Setting up libubsan0:s390x (7.3.0-17ubuntu1) ... Setting up binutils-s390x-linux-gnu (2.30-17ubuntu1) ... Setting up libgcc-7-dev:s390x (7.3.0-17ubuntu1) ... Setting up cpp-7 (7.3.0-17ubuntu1) ... Setting up procps (2:3.3.12-3ubuntu2) ... Setting up libstdc++-7-dev:s390x (7.3.0-17ubuntu1) ... Processing triggers for systemd (237-3ubuntu10) ... Setting up binutils (2.30-17ubuntu1) ... Setting up gcc-7 (7.3.0-17ubuntu1) ... Setting up g++-7 (7.3.0-17ubuntu1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-14825711 s390x cosmic -c chroot:build-PACKAGEBUILD-14825711 --arch=s390x --dist=cosmic --nolog bcftools_1.7-2.dsc Initiating build PACKAGEBUILD-14825711 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-122-generic #146-Ubuntu SMP Mon Apr 23 15:33:03 UTC 2018 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-s390x-008.buildd +==============================================================================+ | bcftools 1.7-2 (s390x) 04 May 2018 16:04 | +==============================================================================+ Package: bcftools Version: 1.7-2 Source Version: 1.7-2 Distribution: cosmic Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/bcftools-jYGCn_/bcftools-1.7' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-jYGCn_' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-14825711/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bcftools_1.7-2.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-grcvY0/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-grcvY0/apt_archive ./ InRelease Get:2 copy:/<>/resolver-grcvY0/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-grcvY0/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-grcvY0/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-grcvY0/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (285 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-grcvY0/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12406 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl Filtered Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<>/resolver-x4sBJ8/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. Ign:1 copy:/<>/resolver-x4sBJ8/apt_archive ./ InRelease Get:2 copy:/<>/resolver-x4sBJ8/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-x4sBJ8/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-x4sBJ8/apt_archive ./ Sources [269 B] Get:5 copy:/<>/resolver-x4sBJ8/apt_archive ./ Packages [573 B] Fetched 2961 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install bcftools build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu60 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libtimedate-perl libtool libwind0-heimdal libxml2 m4 man-db po-debconf tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu60 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libtimedate-perl libtool libwind0-heimdal libxml2 m4 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 21.0 MB of archives. After this operation, 85.0 MB of additional disk space will be used. Get:1 copy:/<>/resolver-x4sBJ8/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [904 B] Get:2 http://ftpmaster.internal/ubuntu cosmic/main s390x libbsd0 s390x 0.8.7-1 [40.0 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main s390x bsdmainutils s390x 11.1.2ubuntu2 [181 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main s390x groff-base s390x 1.22.3-10 [1174 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main s390x libpipeline1 s390x 1.5.0-1 [24.1 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main s390x man-db s390x 2.8.3-2 [1007 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main s390x libmagic-mgc s390x 1:5.32-2 [185 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main s390x libmagic1 s390x 1:5.32-2 [66.9 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main s390x file s390x 1:5.32-2 [21.9 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main s390x libglib2.0-0 s390x 2.56.1-2ubuntu1 [1077 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic/main s390x libicu60 s390x 60.2-3ubuntu3 [7837 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main s390x libxml2 s390x 2.9.4+dfsg1-6.1ubuntu1 [587 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic/main s390x gettext-base s390x 0.19.8.1-6build1 [48.2 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main s390x libkrb5support0 s390x 1.16-2build1 [30.4 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main s390x libk5crypto3 s390x 1.16-2build1 [84.1 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main s390x libkeyutils1 s390x 1.5.9-9.2ubuntu2 [8520 B] Get:17 http://ftpmaster.internal/ubuntu cosmic/main s390x libkrb5-3 s390x 1.16-2build1 [261 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main s390x libgssapi-krb5-2 s390x 1.16-2build1 [110 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main s390x libpsl5 s390x 0.19.1-5build1 [41.5 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic/main s390x libsigsegv2 s390x 2.12-1 [14.6 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main s390x m4 s390x 1.4.18-1 [195 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main s390x autoconf all 2.69-11 [322 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main s390x autotools-dev all 20180224.1 [39.6 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main s390x automake all 1:1.15.1-3ubuntu2 [509 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main s390x autopoint all 0.19.8.1-6build1 [412 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main s390x libtool all 2.4.6-2 [194 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic/main s390x dh-autoreconf all 17 [15.8 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main s390x libarchive-zip-perl all 1.60-1 [83.9 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main s390x libfile-stripnondeterminism-perl all 0.040-1.1~build1 [13.8 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main s390x libtimedate-perl all 2.3000-2 [37.5 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main s390x dh-strip-nondeterminism all 0.040-1.1~build1 [5208 B] Get:32 http://ftpmaster.internal/ubuntu cosmic/main s390x libcroco3 s390x 0.6.12-2 [74.2 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main s390x gettext s390x 0.19.8.1-6build1 [858 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic/main s390x intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic/main s390x po-debconf all 1.0.20 [232 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic/main s390x debhelper all 11.2.1ubuntu1 [906 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic/main s390x libroken18-heimdal s390x 7.5.0+dfsg-1 [39.4 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main s390x libasn1-8-heimdal s390x 7.5.0+dfsg-1 [147 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic/main s390x libbz2-dev s390x 1.0.6-8.1 [30.4 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main s390x libheimbase1-heimdal s390x 7.5.0+dfsg-1 [27.5 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic/main s390x libhcrypto4-heimdal s390x 7.5.0+dfsg-1 [82.4 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main s390x libwind0-heimdal s390x 7.5.0+dfsg-1 [47.7 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main s390x libhx509-5-heimdal s390x 7.5.0+dfsg-1 [98.3 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main s390x libkrb5-26-heimdal s390x 7.5.0+dfsg-1 [190 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main s390x libheimntlm0-heimdal s390x 7.5.0+dfsg-1 [14.1 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main s390x libgssapi3-heimdal s390x 7.5.0+dfsg-1 [86.9 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main s390x libsasl2-modules-db s390x 2.1.27~101-g0780600+dfsg-3ubuntu2 [13.9 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main s390x libsasl2-2 s390x 2.1.27~101-g0780600+dfsg-3ubuntu2 [46.5 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main s390x libldap-common all 2.4.45+dfsg-1ubuntu1 [16.6 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main s390x libldap-2.4-2 s390x 2.4.45+dfsg-1ubuntu1 [144 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main s390x libnghttp2-14 s390x 1.30.0-1ubuntu1 [74.1 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-1 [51.8 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main s390x libcurl3-gnutls s390x 7.58.0-2ubuntu3 [195 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic/universe s390x libgslcblas0 s390x 2.4+dfsg-6 [75.8 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/universe s390x libgsl23 s390x 2.4+dfsg-6 [716 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/universe s390x libgsl-dev s390x 2.4+dfsg-6 [900 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/universe s390x libhts2 s390x 1.7-2 [278 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main s390x liblzma-dev s390x 5.2.2-1.3 [145 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic/universe s390x libhts-dev s390x 1.7-2 [360 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/main s390x libio-pty-perl s390x 1:1.08-1.1build4 [29.4 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic/universe s390x tabix s390x 1.7-2 [297 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic/main s390x zlib1g-dev s390x 1:1.2.11.dfsg-0ubuntu2 [173 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 21.0 MB in 3s (6301 kB/s) Selecting previously unselected package libbsd0:s390x. (Reading database ... 12406 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.8.7-1_s390x.deb ... Unpacking libbsd0:s390x (0.8.7-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu2_s390x.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.3-10_s390x.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../03-libpipeline1_1.5.0-1_s390x.deb ... Unpacking libpipeline1:s390x (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.3-2_s390x.deb ... Unpacking man-db (2.8.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.32-2_s390x.deb ... Unpacking libmagic-mgc (1:5.32-2) ... Selecting previously unselected package libmagic1:s390x. 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Setting up libbz2-dev:s390x (1.0.6-8.1) ... Setting up libarchive-zip-perl (1.60-1) ... Setting up libnghttp2-14:s390x (1.30.0-1ubuntu1) ... Setting up libio-pty-perl (1:1.08-1.1build4) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:s390x (2.12-1) ... Setting up libldap-common (2.4.45+dfsg-1ubuntu1) ... Setting up libpsl5:s390x (0.19.1-5build1) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:s390x (2.56.1-2ubuntu1) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:s390x (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up libsasl2-2:s390x (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up gettext-base (0.19.8.1-6build1) ... Setting up libpipeline1:s390x (1.5.0-1) ... Setting up libroken18-heimdal:s390x (7.5.0+dfsg-1) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:s390x (0.8.7-1) ... Setting up libkrb5support0:s390x (1.16-2build1) ... Setting up libxml2:s390x (2.9.4+dfsg1-6.1ubuntu1) ... Setting up libmagic-mgc (1:5.32-2) ... Setting up libmagic1:s390x (1:5.32-2) ... Setting up libcroco3:s390x (0.6.12-2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:s390x (7.5.0+dfsg-1) ... Setting up liblzma-dev:s390x (5.2.2-1.3) ... Setting up libkeyutils1:s390x (1.5.9-9.2ubuntu2) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgslcblas0:s390x (2.4+dfsg-6) ... Setting up autopoint (0.19.8.1-6build1) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.040-1.1~build1) ... Setting up libk5crypto3:s390x (1.16-2build1) ... Setting up libwind0-heimdal:s390x (7.5.0+dfsg-1) ... Setting up libgsl23:s390x (2.4+dfsg-6) ... Setting up gettext (0.19.8.1-6build1) ... Setting up libgsl-dev (2.4+dfsg-6) ... Setting up libasn1-8-heimdal:s390x (7.5.0+dfsg-1) ... Setting up libhcrypto4-heimdal:s390x (7.5.0+dfsg-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-2) ... Setting up libhx509-5-heimdal:s390x (7.5.0+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libkrb5-3:s390x (1.16-2build1) ... Setting up libkrb5-26-heimdal:s390x (7.5.0+dfsg-1) ... Setting up libheimntlm0-heimdal:s390x (7.5.0+dfsg-1) ... Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up libgssapi-krb5-2:s390x (1.16-2build1) ... Setting up libgssapi3-heimdal:s390x (7.5.0+dfsg-1) ... Setting up libldap-2.4-2:s390x (2.4.45+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:s390x (7.58.0-2ubuntu3) ... Setting up tabix (1.7-2) ... Setting up libhts2:s390x (1.7-2) ... Setting up libhts-dev:s390x (1.7-2) ... Setting up dh-autoreconf (17) ... Setting up dh-strip-nondeterminism (0.040-1.1~build1) ... Setting up debhelper (11.2.1ubuntu1) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-122-generic s390x (s390x) Toolchain package versions: binutils_2.30-17ubuntu1 dpkg-dev_1.19.0.5ubuntu2 g++-7_7.3.0-17ubuntu1 gcc-7_7.3.0-17ubuntu1 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-17ubuntu1 libstdc++6_8.1.0-1ubuntu2 linux-libc-dev_4.15.0-20.21 Package versions: adduser_3.116ubuntu1 advancecomp_2.1-1 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6build1 autotools-dev_20180224.1 base-files_10.1ubuntu3 base-passwd_3.5.44 bash_4.4.18-2ubuntu2 binutils_2.30-17ubuntu1 binutils-common_2.30-17ubuntu1 binutils-s390x-linux-gnu_2.30-17ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.31.1-0.4ubuntu3 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20180409 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu2 cpp-7_7.3.0-17ubuntu1 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.2.1ubuntu1 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.040-1.1~build1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu2 dpkg-dev_1.19.0.5ubuntu2 e2fslibs_1.44.1-1 e2fsprogs_1.44.1-1 fakeroot_1.22-2ubuntu1 fdisk_2.31.1-0.4ubuntu3 file_1:5.32-2 findutils_4.6.0+git+20170828-2 g++_4:7.3.0-3ubuntu2 g++-7_7.3.0-17ubuntu1 gcc_4:7.3.0-3ubuntu2 gcc-7_7.3.0-17ubuntu1 gcc-7-base_7.3.0-17ubuntu1 gcc-8-base_8.1.0-1ubuntu2 gettext_0.19.8.1-6build1 gettext-base_0.19.8.1-6build1 gpg_2.2.4-1ubuntu1 gpg-agent_2.2.4-1ubuntu1 gpgconf_2.2.4-1ubuntu1 gpgv_2.2.4-1ubuntu1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hostname_3.20 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu5 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-1.1 libasan4_7.3.0-17ubuntu1 libasn1-8-heimdal_7.5.0+dfsg-1 libassuan0_2.5.1-2 libatomic1_8.1.0-1ubuntu2 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.2-1ubuntu1 libaudit1_1:2.8.2-1ubuntu1 libbinutils_2.30-17ubuntu1 libblkid1_2.31.1-0.4ubuntu3 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcap-ng0_0.7.7-3.1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-1ubuntu2 libcom-err2_1.44.1-1 libcomerr2_1.44.1-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu1 libcurl3-gnutls_7.58.0-2ubuntu3 libdb5.3_5.3.28-13.1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu2 libext2fs2_1.44.1-1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.31.1-0.4ubuntu3 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1.1~build1 libgcc-7-dev_7.3.0-17ubuntu1 libgcc1_1:8.1.0-1ubuntu2 libgcrypt20_1.8.1-4ubuntu1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2ubuntu1 libgmp10_2:6.1.2+dfsg-2 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.1.0-1ubuntu2 libgpg-error0_1.27-6 libgsl-dev_2.4+dfsg-6 libgsl23_2.4+dfsg-6 libgslcblas0_2.4+dfsg-6 libgssapi-krb5-2_1.16-2build1 libgssapi3-heimdal_7.5.0+dfsg-1 libhcrypto4-heimdal_7.5.0+dfsg-1 libheimbase1-heimdal_7.5.0+dfsg-1 libheimntlm0-heimdal_7.5.0+dfsg-1 libhogweed4_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libhx509-5-heimdal_7.5.0+dfsg-1 libicu60_60.2-3ubuntu3 libidn11_1.33-2.1ubuntu1 libidn2-0_2.0.4-1.1build2 libio-pty-perl_1:1.08-1.1build4 libip4tc0_1.6.1-2ubuntu2 libisl19_0.19-1 libitm1_8.1.0-1ubuntu2 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2build1 libkeyutils1_1.5.9-9.2ubuntu2 libkmod2_24-1ubuntu3 libkrb5-26-heimdal_7.5.0+dfsg-1 libkrb5-3_1.16-2build1 libkrb5support0_1.16-2build1 libldap-2.4-2_2.4.45+dfsg-1ubuntu1 libldap-common_2.4.45+dfsg-1ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblz4-1_0.0~r131-2ubuntu3 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2 libmagic1_1:5.32-2 libmount1_2.31.1-0.4ubuntu3 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180210-2ubuntu2 libncurses6_6.1+20180210-2ubuntu2 libncursesw5_6.1+20180210-2ubuntu2 libncursesw6_6.1+20180210-2ubuntu2 libnettle6_3.4-1 libnghttp2-14_1.30.0-1ubuntu1 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-9 libperl5.26_5.26.1-6 libpipeline1_1.5.0-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3ubuntu2 libpsl5_0.19.1-5build1 libreadline7_7.0-4 libroken18-heimdal_7.5.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.1-2.1ubuntu4 libselinux1_2.7-2build2 libsemanage-common_2.7-2build2 libsemanage1_2.7-2build2 libsepol1_2.7-1 libsigsegv2_2.12-1 libslang2_2.3.1a-3ubuntu1 libsmartcols1_2.31.1-0.4ubuntu3 libsqlite3-0_3.22.0-1 libss2_1.44.1-1 libssl1.1_1.1.0g-2ubuntu4 libstdc++-7-dev_7.3.0-17ubuntu1 libstdc++6_8.1.0-1ubuntu2 libsystemd0_237-3ubuntu10 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-2ubuntu2 libtinfo6_6.1+20180210-2ubuntu2 libtool_2.4.6-2 libubsan0_7.3.0-17ubuntu1 libudev1_237-3ubuntu10 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.4ubuntu3 libwind0-heimdal_7.5.0+dfsg-1 libxml2_2.9.4+dfsg1-6.1ubuntu1 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.15.0-20.21 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2 mawk_1.3.3-17ubuntu3 mount_2.31.1-0.4ubuntu3 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1+20180210-2ubuntu2 ncurses-bin_6.1+20180210-2ubuntu2 openssl_1.1.0g-2ubuntu4 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.1-6 perl-base_5.26.1-6 perl-modules-5.26_5.26.1-6 pinentry-curses_1.1.0-1 pkgbinarymangler_138 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu2 readline-common_7.0-4 sbuild-build-depends-bcftools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_237-3ubuntu10 systemd-sysv_237-3ubuntu10 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tabix_1.7-2 tar_1.29b-2 tzdata_2018d-1 ubuntu-keyring_2018.02.28 util-linux_2.31.1-0.4ubuntu3 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Feb 20 15:51:47 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.7-2.dsc dpkg-source: info: extracting bcftools in bcftools-1.7 dpkg-source: info: unpacking bcftools_1.7.orig.tar.gz dpkg-source: info: unpacking bcftools_1.7-2.debian.tar.xz dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-14825711 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-14825711 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-14825711 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.7-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build bcftools-1.7 dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean rm -f config.mk && touch config.mk dh clean dh_auto_clean make -j4 -Oline distclean make[1]: Entering directory '/<>' rm -f plugins/*.so plugins/*.P make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' rm -rf plugins/*.dSYM make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' rm -f gmon.out *.o *~ bcftools version.h plugins/*.so plugins/*.P make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' rm -rf *.dSYM plugins/*.dSYM test/*.dSYM make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' rm -f config.cache config.h config.log config.mk config.status make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' rm -rf autom4te.cache make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' rm -f TAGS make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/<>' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:81: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:81: the top level configure.ac:81: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:81: the top level configure.ac:81: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:81: the top level configure.ac:81: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:81: the top level make[1]: Leaving directory '/<>' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/s390x-linux-gnu/bcftools ./configure --build=s390x-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/s390x-linux-gnu --libexecdir=\${prefix}/lib/s390x-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/s390x-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/<>' dh_auto_build -a make -j4 -Oline make[1]: Entering directory '/<>' echo '#define BCFTOOLS_VERSION "1.7"' > version.h make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/s390x-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/split.so version.c plugins/split.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -rdynamic -pthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o ccall.o em.o prob1.o kmin.o -lhts -lm -lz -ldl -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl make[1]: Leaving directory '/<>' dh_auto_test -a make -j4 -Oline test VERBOSE=1 make[1]: Entering directory '/<>' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' ./test/test-regidx make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix= test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/ZuB8TSuaoL/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/ZuB8TSuaoL/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/ZuB8TSuaoL/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/ZuB8TSuaoL/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/ZuB8TSuaoL/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/ZuB8TSuaoL/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/ZuB8TSuaoL/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/ZuB8TSuaoL/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/ZuB8TSuaoL/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/ZuB8TSuaoL/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/ZuB8TSuaoL/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/ZuB8TSuaoL/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/ZuB8TSuaoL/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/ZuB8TSuaoL/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/ZuB8TSuaoL/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/ZuB8TSuaoL/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/ZuB8TSuaoL/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZuB8TSuaoL/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZuB8TSuaoL/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZuB8TSuaoL/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/ZuB8TSuaoL/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/ZuB8TSuaoL/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/ZuB8TSuaoL/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZuB8TSuaoL/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZuB8TSuaoL/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZuB8TSuaoL/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/ZuB8TSuaoL/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/check.vcf.gz | /<>/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /<>/misc/plot-vcfstats -m /tmp/ZuB8TSuaoL/check.1.chk /tmp/ZuB8TSuaoL/check.2.chk /tmp/ZuB8TSuaoL/check.3.chk /tmp/ZuB8TSuaoL/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/ZuB8TSuaoL/stats.a.vcf.gz /tmp/ZuB8TSuaoL/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/ZuB8TSuaoL/stats.a.vcf.gz /tmp/ZuB8TSuaoL/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/ZuB8TSuaoL/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/ZuB8TSuaoL/isec.a.vcf.gz /tmp/ZuB8TSuaoL/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/ZuB8TSuaoL/isec.a.vcf.gz /tmp/ZuB8TSuaoL/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/ZuB8TSuaoL/isec.a.vcf.gz /tmp/ZuB8TSuaoL/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/ZuB8TSuaoL/isec.a.vcf.gz /tmp/ZuB8TSuaoL/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/ZuB8TSuaoL/isec.a.vcf.gz /tmp/ZuB8TSuaoL/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/ZuB8TSuaoL/isec.a.vcf.gz /tmp/ZuB8TSuaoL/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/ZuB8TSuaoL/isec.a.vcf.gz /tmp/ZuB8TSuaoL/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/ZuB8TSuaoL/isec.a.vcf.gz /tmp/ZuB8TSuaoL/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/ZuB8TSuaoL/isec.a.vcf.gz /tmp/ZuB8TSuaoL/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/ZuB8TSuaoL/isec.a.vcf.gz /tmp/ZuB8TSuaoL/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/ZuB8TSuaoL/isec.tab.gz /tmp/ZuB8TSuaoL/isec.a.vcf.gz 2>/dev/null The outputs differ: /<>/test/isec.tab.out /<>/test/isec.tab.out.new .. failed ... test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/ZuB8TSuaoL/isec.tab.gz /tmp/ZuB8TSuaoL/isec.a.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/isec.tab.out /<>/test/isec.tab.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/ZuB8TSuaoL/merge.a.vcf.gz /tmp/ZuB8TSuaoL/merge.b.vcf.gz /tmp/ZuB8TSuaoL/merge.c.vcf.gz The outputs differ: /<>/test/merge.abc.out /<>/test/merge.abc.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/ZuB8TSuaoL/merge.a.vcf.gz /tmp/ZuB8TSuaoL/merge.b.vcf.gz /tmp/ZuB8TSuaoL/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.abc.out /<>/test/merge.abc.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/ZuB8TSuaoL/merge.a.vcf.gz /tmp/ZuB8TSuaoL/merge.b.vcf.gz /tmp/ZuB8TSuaoL/merge.c.vcf.gz The outputs differ: /<>/test/merge.abc.2.out /<>/test/merge.abc.2.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -Fx /tmp/ZuB8TSuaoL/merge.a.vcf.gz /tmp/ZuB8TSuaoL/merge.b.vcf.gz /tmp/ZuB8TSuaoL/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.abc.2.out /<>/test/merge.abc.2.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/ZuB8TSuaoL/merge.a.vcf.gz /tmp/ZuB8TSuaoL/merge.b.vcf.gz /tmp/ZuB8TSuaoL/merge.c.vcf.gz The outputs differ: /<>/test/merge.abc.3.out /<>/test/merge.abc.3.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -0 /tmp/ZuB8TSuaoL/merge.a.vcf.gz /tmp/ZuB8TSuaoL/merge.b.vcf.gz /tmp/ZuB8TSuaoL/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.abc.3.out /<>/test/merge.abc.3.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/ZuB8TSuaoL/merge.2.a.vcf.gz /tmp/ZuB8TSuaoL/merge.2.b.vcf.gz The outputs differ: /<>/test/merge.2.none.out /<>/test/merge.2.none.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m none /tmp/ZuB8TSuaoL/merge.2.a.vcf.gz /tmp/ZuB8TSuaoL/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.2.none.out /<>/test/merge.2.none.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/ZuB8TSuaoL/merge.2.a.vcf.gz /tmp/ZuB8TSuaoL/merge.2.b.vcf.gz The outputs differ: /<>/test/merge.2.both.out /<>/test/merge.2.both.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m both /tmp/ZuB8TSuaoL/merge.2.a.vcf.gz /tmp/ZuB8TSuaoL/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.2.both.out /<>/test/merge.2.both.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/ZuB8TSuaoL/merge.2.a.vcf.gz /tmp/ZuB8TSuaoL/merge.2.b.vcf.gz The outputs differ: /<>/test/merge.2.all.out /<>/test/merge.2.all.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m all /tmp/ZuB8TSuaoL/merge.2.a.vcf.gz /tmp/ZuB8TSuaoL/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.2.all.out /<>/test/merge.2.all.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/ZuB8TSuaoL/merge.3.a.vcf.gz /tmp/ZuB8TSuaoL/merge.3.b.vcf.gz The outputs differ: /<>/test/merge.3.out /<>/test/merge.3.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/ZuB8TSuaoL/merge.3.a.vcf.gz /tmp/ZuB8TSuaoL/merge.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.3.out /<>/test/merge.3.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/ZuB8TSuaoL/merge.4.a.vcf.gz /tmp/ZuB8TSuaoL/merge.4.b.vcf.gz The outputs differ: /<>/test/merge.4.out /<>/test/merge.4.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m id /tmp/ZuB8TSuaoL/merge.4.a.vcf.gz /tmp/ZuB8TSuaoL/merge.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.4.out /<>/test/merge.4.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZuB8TSuaoL/gvcf.merge.1.vcf.gz /tmp/ZuB8TSuaoL/gvcf.merge.2.vcf.gz /tmp/ZuB8TSuaoL/gvcf.merge.3.vcf.gz The outputs differ: /<>/test/gvcf.merge.1.out /<>/test/gvcf.merge.1.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/ZuB8TSuaoL/gvcf.merge.1.vcf.gz /tmp/ZuB8TSuaoL/gvcf.merge.2.vcf.gz /tmp/ZuB8TSuaoL/gvcf.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/gvcf.merge.1.out /<>/test/gvcf.merge.1.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZuB8TSuaoL/merge.gvcf.2.a.vcf.gz /tmp/ZuB8TSuaoL/merge.gvcf.2.b.vcf.gz /tmp/ZuB8TSuaoL/merge.gvcf.2.c.vcf.gz The outputs differ: /<>/test/merge.gvcf.2.out /<>/test/merge.gvcf.2.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/ZuB8TSuaoL/merge.gvcf.2.a.vcf.gz /tmp/ZuB8TSuaoL/merge.gvcf.2.b.vcf.gz /tmp/ZuB8TSuaoL/merge.gvcf.2.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.gvcf.2.out /<>/test/merge.gvcf.2.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/ZuB8TSuaoL/merge.gvcf.3.a.vcf.gz /tmp/ZuB8TSuaoL/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/ZuB8TSuaoL/merge.gvcf.3.a.vcf.gz /tmp/ZuB8TSuaoL/merge.gvcf.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZuB8TSuaoL/merge.5.a.vcf.gz /tmp/ZuB8TSuaoL/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/ZuB8TSuaoL/merge.5.a.vcf.gz /tmp/ZuB8TSuaoL/merge.5.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/ZuB8TSuaoL/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /<>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/ZuB8TSuaoL/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.vcf.gz | /<>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /<>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/ZuB8TSuaoL/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.vcf.gz | /<>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /<>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/ZuB8TSuaoL/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.vcf.gz | /<>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/ZuB8TSuaoL/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.vcf.gz | /<>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /<>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/ZuB8TSuaoL/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/ZuB8TSuaoL/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/ZuB8TSuaoL/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/ZuB8TSuaoL/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /<>/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/ZuB8TSuaoL/view.vectors.vcf.gz The outputs differ: /<>/test/query.12.out /<>/test/query.12.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.vectors.vcf.gz | /<>/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' The outputs differ: /<>/test/query.12.out /<>/test/query.12.out.new .. failed ... test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/ZuB8TSuaoL/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/ZuB8TSuaoL/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/ZuB8TSuaoL/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/ZuB8TSuaoL/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/ZuB8TSuaoL/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.2.vcf.gz | /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/ZuB8TSuaoL/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/ZuB8TSuaoL/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/ZuB8TSuaoL/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/ZuB8TSuaoL/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/ZuB8TSuaoL/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/ZuB8TSuaoL/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/filter-missing-floats.vcf.gz | /<>/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/ZuB8TSuaoL/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/filter-missing-floats.vcf.gz | /<>/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /<>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/ZuB8TSuaoL/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/missing.vcf.gz | /<>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /<>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/ZuB8TSuaoL/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter.2.vcf.gz | /<>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/ZuB8TSuaoL/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/filter.5.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/ZuB8TSuaoL/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/filter.5.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/ZuB8TSuaoL/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter.3.vcf.gz | /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/ZuB8TSuaoL/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter.3.vcf.gz | /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/ZuB8TSuaoL/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter.3.vcf.gz | /<>/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/ZuB8TSuaoL/query.filter.4.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/query.filter.4.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx -f /<>/test/norm.fa /tmp/ZuB8TSuaoL/norm.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.out /<>/test/norm.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -cx -f /<>/test/norm.fa /tmp/ZuB8TSuaoL/norm.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.out /<>/test/norm.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/ZuB8TSuaoL/norm.split.vcf.gz 2>/dev/null Non-zero status 1 .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/ZuB8TSuaoL/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ [E::bcf_record_check] Bad BCF record - shared section malformed or too short The outputs differ: /<>/test/norm.split.out /<>/test/norm.split.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/ZuB8TSuaoL/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/ZuB8TSuaoL/norm.split.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- -f /<>/test/norm.fa /tmp/ZuB8TSuaoL/norm.split.vcf.gz 2>/dev/null Non-zero status 255 .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m- -f /<>/test/norm.fa /tmp/ZuB8TSuaoL/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ Failed to open -: unknown file type Non-zero status 1 .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/ZuB8TSuaoL/norm.merge.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.merge.out /<>/test/norm.merge.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/ZuB8TSuaoL/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ [E::bcf_record_check] Bad BCF record - shared section malformed or too short The outputs differ: /<>/test/norm.merge.out /<>/test/norm.merge.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/ZuB8TSuaoL/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/ZuB8TSuaoL/norm.merge.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/ZuB8TSuaoL/norm.merge.3.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/ZuB8TSuaoL/norm.merge.3.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/ZuB8TSuaoL/norm.merge.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.merge.strict.out /<>/test/norm.merge.strict.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ -s /tmp/ZuB8TSuaoL/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ [E::bcf_record_check] Bad BCF record - shared section malformed or too short The outputs differ: /<>/test/norm.merge.strict.out /<>/test/norm.merge.strict.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -Nc s -f /<>/test/norm.fa /tmp/ZuB8TSuaoL/norm.setref.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/ZuB8TSuaoL/norm.setref.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.fa /tmp/ZuB8TSuaoL/norm.telomere.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/ZuB8TSuaoL/norm.telomere.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/ZuB8TSuaoL/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d snps /tmp/ZuB8TSuaoL/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/ZuB8TSuaoL/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d indels /tmp/ZuB8TSuaoL/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/ZuB8TSuaoL/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d both /tmp/ZuB8TSuaoL/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/ZuB8TSuaoL/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d all /tmp/ZuB8TSuaoL/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/ZuB8TSuaoL/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d none /tmp/ZuB8TSuaoL/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/ZuB8TSuaoL/view.vcf.gz The outputs differ: /<>/test/view.1.out /<>/test/view.1.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/ZuB8TSuaoL/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.1.out /<>/test/view.1.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/ZuB8TSuaoL/view.vcf.gz -r20,Y The outputs differ: /<>/test/view.2.out /<>/test/view.2.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/ZuB8TSuaoL/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.2.out /<>/test/view.2.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/ZuB8TSuaoL/view.vcf.gz The outputs differ: /<>/test/view.3.out /<>/test/view.3.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/ZuB8TSuaoL/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.3.out /<>/test/view.3.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/ZuB8TSuaoL/view.vcf.gz The outputs differ: /<>/test/view.4.out /<>/test/view.4.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/ZuB8TSuaoL/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.4.out /<>/test/view.4.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -p /tmp/ZuB8TSuaoL/view.vcf.gz The outputs differ: /<>/test/view.5.out /<>/test/view.5.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -p /tmp/ZuB8TSuaoL/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.5.out /<>/test/view.5.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -P /tmp/ZuB8TSuaoL/view.vcf.gz The outputs differ: /<>/test/view.6.out /<>/test/view.6.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -P /tmp/ZuB8TSuaoL/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.6.out /<>/test/view.6.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/ZuB8TSuaoL/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/ZuB8TSuaoL/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/ZuB8TSuaoL/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/ZuB8TSuaoL/view.vcf.gz The outputs differ: /<>/test/view.9.out /<>/test/view.9.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/ZuB8TSuaoL/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.9.out /<>/test/view.9.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/ZuB8TSuaoL/view.vcf.gz The outputs differ: /<>/test/view.10.out /<>/test/view.10.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/ZuB8TSuaoL/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.10.out /<>/test/view.10.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/ZuB8TSuaoL/view.vcf.gz The outputs differ: /<>/test/view.exclude.out /<>/test/view.exclude.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/ZuB8TSuaoL/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.exclude.out /<>/test/view.exclude.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version /tmp/ZuB8TSuaoL/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/ZuB8TSuaoL/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/ZuB8TSuaoL/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/ZuB8TSuaoL/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/ZuB8TSuaoL/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/ZuB8TSuaoL/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/ZuB8TSuaoL/view.vectors.vcf.gz The outputs differ: /<>/test/view.vectors.A.out /<>/test/view.vectors.A.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -asA /tmp/ZuB8TSuaoL/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.vectors.A.out /<>/test/view.vectors.A.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -asB /tmp/ZuB8TSuaoL/view.vectors.vcf.gz The outputs differ: /<>/test/view.vectors.B.out /<>/test/view.vectors.B.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -asB /tmp/ZuB8TSuaoL/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.vectors.B.out /<>/test/view.vectors.B.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -asA /tmp/ZuB8TSuaoL/view.vectors.2.vcf.gz [E::bcf_remove_allele_set] Unexpected number of values in INFO/IAF at 1:10; expected Number=A=2, but found 1 Error: Could not trim alleles at 1:10 Non-zero status 255 .. failed ... test_vcf_view: /<>/bcftools view -Ob -asA /tmp/ZuB8TSuaoL/view.vectors.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ [E::bcf_remove_allele_set] Unexpected number of values in INFO/IAF at 1:10; expected Number=A=2, but found 1 Error: Could not trim alleles at 1:10 Failed to open -: unknown file type Non-zero status 1 .. failed ... test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/ZuB8TSuaoL/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/ZuB8TSuaoL/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/ZuB8TSuaoL/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/ZuB8TSuaoL/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/ZuB8TSuaoL/filter.2.vcf.gz 1:3062917-3157410 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'TXT0="text"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'TXT0="text"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/STR="XX"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/STR="XX"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -C5:nonmajor /tmp/ZuB8TSuaoL/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/ZuB8TSuaoL/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/ZuB8TSuaoL/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/ZuB8TSuaoL/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/ZuB8TSuaoL/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/ZuB8TSuaoL/view.filter.annovar.vcf.gz .. ok test_vcf_call: /<>/bcftools call --no-version -mv /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv /<>/test/mpileup.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mg0 /<>/test/mpileup.vcf 2>/dev/null The outputs differ: /<>/test/mpileup.2.out /<>/test/mpileup.2.out.new .. failed ... test_vcf_call: /<>/bcftools call -Ob -mg0 /<>/test/mpileup.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/mpileup.2.out /<>/test/mpileup.2.out.new .. failed ... test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/ZuB8TSuaoL/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/ZuB8TSuaoL/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv /<>/test/mpileup.c.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv /<>/test/mpileup.c.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.c.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.c.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.c.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -mx -g2 -G2 /<>/test/filter.1.vcf | grep -v ^##bcftools_ The outputs differ: /<>/test/filter.1.out /<>/test/filter.1.out.new .. failed ... test_vcf_filter: /<>/bcftools filter -Ob -mx -g2 -G2 /<>/test/filter.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/filter.1.out /<>/test/filter.1.out.new .. failed ... test_vcf_filter: /<>/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<>/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<>/test/filter.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'ALT="."' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'ALT="."' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -S . -i 'FORMAT/TEST3<25' /<>/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /<>/test/filter.4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -i 'FORMAT/TEST4<25' /<>/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /<>/test/filter.4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i'GT="A"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="A"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="RR"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="RR"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="RA"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="RA"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="AR"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="AR"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="AA"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="AA"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="aA"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="aA"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="Aa"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="Aa"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="HOM"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="HOM"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="HET"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="HET"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="HAP"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="HAP"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[:1]=11' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[:1]=11' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[1:]=11' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[1:]=11' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'FR[0:1]=11' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'FR[0:1]=11' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[*]="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[*]="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[0:0]=="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[0:0]=="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[0:0]!="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[0:0]!="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'QUAL=="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'QUAL=="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_sort: /<>/bcftools sort -m 0 /<>/test/sort.vcf | /<>/bcftools query -f '%CHROM\t%POS\n' Writing to /tmp/bcftools-sort.EesCT7 Merging 15 temporary files Cleaning Done .. ok test_vcf_sort: /<>/bcftools sort -Ob -m 0 /<>/test/sort.vcf | /<>/bcftools view | /<>/bcftools query -f '%CHROM\t%POS\n' Writing to /tmp/bcftools-sort.vHYZ2a Merging 15 temporary files Cleaning Done .. ok test_vcf_sort: /<>/bcftools sort -m 1000 /<>/test/sort.vcf | /<>/bcftools query -f '%CHROM\t%POS\n' Writing to /tmp/bcftools-sort.pmyaJ9 Merging 4 temporary files Cleaning Done .. ok test_vcf_sort: /<>/bcftools sort -Ob -m 1000 /<>/test/sort.vcf | /<>/bcftools view | /<>/bcftools query -f '%CHROM\t%POS\n' Writing to /tmp/bcftools-sort.Gkrjxd Merging 4 temporary files Cleaning Done .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab /tmp/ZuB8TSuaoL/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /<>/test/regions.tab /tmp/ZuB8TSuaoL/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ZuB8TSuaoL/regions.tab.gz /tmp/ZuB8TSuaoL/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ZuB8TSuaoL/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/ZuB8TSuaoL/regions.tab.gz /tmp/ZuB8TSuaoL/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ZuB8TSuaoL/regions.bed /tmp/ZuB8TSuaoL/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ZuB8TSuaoL/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/ZuB8TSuaoL/regions.bed /tmp/ZuB8TSuaoL/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ZuB8TSuaoL/regions.bed.gz /tmp/ZuB8TSuaoL/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ZuB8TSuaoL/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/ZuB8TSuaoL/regions.bed.gz /tmp/ZuB8TSuaoL/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/ZuB8TSuaoL/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/ZuB8TSuaoL/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/ZuB8TSuaoL/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/ZuB8TSuaoL/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/ZuB8TSuaoL/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/ZuB8TSuaoL/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x FORMAT /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x FORMAT /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annots4.vcf.gz -c +INFO /tmp/ZuB8TSuaoL/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annots4.vcf.gz -c +INFO /tmp/ZuB8TSuaoL/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annots10.tab.gz -h /<>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<>/test/annotate10.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annots10.tab.gz -h /<>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<>/test/annotate10.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/ZuB8TSuaoL/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/ZuB8TSuaoL/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<>/test/annotate2.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<>/test/annotate2.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/ZuB8TSuaoL/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/ZuB8TSuaoL/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/ZuB8TSuaoL/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/ZuB8TSuaoL/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/ZuB8TSuaoL/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/ZuB8TSuaoL/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +missing2ref --no-version /tmp/ZuB8TSuaoL/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +missing2ref --no-version /tmp/ZuB8TSuaoL/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/ZuB8TSuaoL/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/ZuB8TSuaoL/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/ZuB8TSuaoL/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/ZuB8TSuaoL/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZuB8TSuaoL/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZuB8TSuaoL/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-AN-AC --no-version /tmp/ZuB8TSuaoL/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-AN-AC --no-version /tmp/ZuB8TSuaoL/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +dosage /tmp/ZuB8TSuaoL/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +dosage /tmp/ZuB8TSuaoL/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixploidy --no-version /tmp/ZuB8TSuaoL/fixploidy.vcf.gz -- -s /<>/test/fixploidy.samples -p /<>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixploidy --no-version /tmp/ZuB8TSuaoL/fixploidy.bcf -- -s /<>/test/fixploidy.samples -p /<>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/ZuB8TSuaoL/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/ZuB8TSuaoL/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/ZuB8TSuaoL/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ Warning: PL tag not found in header, switching to GL .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/ZuB8TSuaoL/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ Warning: PL tag not found in header, switching to GL .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/ZuB8TSuaoL/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/ZuB8TSuaoL/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/ZuB8TSuaoL/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/ZuB8TSuaoL/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/ZuB8TSuaoL/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/ZuB8TSuaoL/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/ZuB8TSuaoL/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/fill-tags.2.out /<>/test/fill-tags.2.out.new .. failed ... test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/ZuB8TSuaoL/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/fill-tags.2.out /<>/test/fill-tags.2.out.new .. failed ... test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/ZuB8TSuaoL/view.vcf.gz -- -t AC -S /<>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/fill-tags.3.out /<>/test/fill-tags.3.out.new .. failed ... test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/ZuB8TSuaoL/view.bcf -- -t AC -S /<>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/fill-tags.3.out /<>/test/fill-tags.3.out.new .. failed ... test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/ZuB8TSuaoL/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/ZuB8TSuaoL/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/ZuB8TSuaoL/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/ZuB8TSuaoL/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/ZuB8TSuaoL/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +trio-switch-rate /tmp/ZuB8TSuaoL/trio.vcf.gz -- -p /<>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +trio-switch-rate /tmp/ZuB8TSuaoL/trio.bcf -- -p /<>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +ad-bias /tmp/ZuB8TSuaoL/ad-bias.vcf.gz -- -s /<>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +ad-bias /tmp/ZuB8TSuaoL/ad-bias.bcf -- -s /<>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +af-dist /tmp/ZuB8TSuaoL/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +af-dist /tmp/ZuB8TSuaoL/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixref /tmp/ZuB8TSuaoL/fixref.2a.vcf.gz -- -f /<>/test/norm.fa -i /tmp/ZuB8TSuaoL/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixref /tmp/ZuB8TSuaoL/fixref.2a.bcf -- -f /<>/test/norm.fa -i /tmp/ZuB8TSuaoL/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/ZuB8TSuaoL/aa.vcf.gz -- -f /<>/test/aa.fa -c AA -h /<>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/aa.out /<>/test/aa.out.new .. failed ... [E::bcf_record_check] Bad BCF record - shared section malformed or too short test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/ZuB8TSuaoL/aa.bcf -- -f /<>/test/aa.fa -c AA -h /<>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/aa.out /<>/test/aa.out.new .. failed ... test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/ZuB8TSuaoL/ref.vcf.gz -- -f /<>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ Non-zero status 1 .. failed ... [E::bcf_record_check] Bad BCF record - shared section malformed or too short test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/ZuB8TSuaoL/ref.bcf -- -f /<>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/ref.out /<>/test/ref.out.new .. failed ... test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/ZuB8TSuaoL/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/view.GTsubset.NA1.out /<>/test/view.GTsubset.NA1.out.new .. failed ... test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/ZuB8TSuaoL/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/view.GTsubset.NA1.out /<>/test/view.GTsubset.NA1.out.new .. failed ... test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/ZuB8TSuaoL/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/view.GTsubset.NA1NA2.out /<>/test/view.GTsubset.NA1NA2.out.new .. failed ... test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/ZuB8TSuaoL/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/view.GTsubset.NA1NA2.out /<>/test/view.GTsubset.NA1NA2.out.new .. failed ... test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/ZuB8TSuaoL/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/view.GTsubset.NA1NA2NA3.out /<>/test/view.GTsubset.NA1NA2NA3.out.new .. failed ... test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/ZuB8TSuaoL/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/view.GTsubset.NA1NA2NA3.out /<>/test/view.GTsubset.NA1NA2NA3.out.new .. failed ... test_vcf_plugin: /<>/bcftools +mendelian /tmp/ZuB8TSuaoL/mendelian.vcf.gz -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/ZuB8TSuaoL/mendelian.bcf -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/ZuB8TSuaoL/mendelian.vcf.gz -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/ZuB8TSuaoL/mendelian.bcf -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/ZuB8TSuaoL/mendelian.vcf.gz -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/ZuB8TSuaoL/mendelian.bcf -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/ZuB8TSuaoL/concat.1.a.vcf.gz /tmp/ZuB8TSuaoL/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/ZuB8TSuaoL/concat.1.a.vcf.gz /tmp/ZuB8TSuaoL/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/concat.1.vcf.out /<>/test/concat.1.vcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat --no-version /tmp/ZuB8TSuaoL/concat.1.a.bcf /tmp/ZuB8TSuaoL/concat.1.b.bcf The outputs differ: /<>/test/concat.1.bcf.out /<>/test/concat.1.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob /tmp/ZuB8TSuaoL/concat.1.a.bcf /tmp/ZuB8TSuaoL/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/concat.1.bcf.out /<>/test/concat.1.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/ZuB8TSuaoL/concat.2.a.vcf.gz /tmp/ZuB8TSuaoL/concat.2.b.vcf.gz The outputs differ: /<>/test/concat.2.vcf.out /<>/test/concat.2.vcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/ZuB8TSuaoL/concat.2.a.vcf.gz /tmp/ZuB8TSuaoL/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/concat.2.vcf.out /<>/test/concat.2.vcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/ZuB8TSuaoL/concat.2.a.bcf /tmp/ZuB8TSuaoL/concat.2.b.bcf The outputs differ: /<>/test/concat.2.bcf.out /<>/test/concat.2.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/ZuB8TSuaoL/concat.2.a.bcf /tmp/ZuB8TSuaoL/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/concat.2.bcf.out /<>/test/concat.2.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/ZuB8TSuaoL/concat.2.a.vcf.gz /tmp/ZuB8TSuaoL/concat.2.b.vcf.gz The outputs differ: /<>/test/concat.4.vcf.out /<>/test/concat.4.vcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/ZuB8TSuaoL/concat.2.a.vcf.gz /tmp/ZuB8TSuaoL/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/concat.4.vcf.out /<>/test/concat.4.vcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/ZuB8TSuaoL/concat.2.a.bcf /tmp/ZuB8TSuaoL/concat.2.b.bcf The outputs differ: /<>/test/concat.4.bcf.out /<>/test/concat.4.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/ZuB8TSuaoL/concat.2.a.bcf /tmp/ZuB8TSuaoL/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/concat.4.bcf.out /<>/test/concat.4.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/ZuB8TSuaoL/concat.3.a.vcf.gz /tmp/ZuB8TSuaoL/concat.3.b.vcf.gz /tmp/ZuB8TSuaoL/concat.3.0.vcf.gz /tmp/ZuB8TSuaoL/concat.3.c.vcf.gz /tmp/ZuB8TSuaoL/concat.3.d.vcf.gz /tmp/ZuB8TSuaoL/concat.3.e.vcf.gz /tmp/ZuB8TSuaoL/concat.3.f.vcf.gz [E::vcf_format] Invalid BCF, the FORMAT tag id=-13056 not present in the header The outputs differ: /<>/test/concat.3.vcf.out /<>/test/concat.3.vcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/ZuB8TSuaoL/concat.3.a.vcf.gz /tmp/ZuB8TSuaoL/concat.3.b.vcf.gz /tmp/ZuB8TSuaoL/concat.3.0.vcf.gz /tmp/ZuB8TSuaoL/concat.3.c.vcf.gz /tmp/ZuB8TSuaoL/concat.3.d.vcf.gz /tmp/ZuB8TSuaoL/concat.3.e.vcf.gz /tmp/ZuB8TSuaoL/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ GT is not present at 2:280. (This warning is printed only once.) [W::bcf_record_check] Bad BCF record: Invalid FORMAT id -13056 The outputs differ: /<>/test/concat.3.vcf.out /<>/test/concat.3.vcf.out.new .. failed ... [W::bcf_record_check] Bad BCF record: Invalid INFO id -14336 [W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080 test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/ZuB8TSuaoL/concat.3.a.bcf /tmp/ZuB8TSuaoL/concat.3.b.bcf /tmp/ZuB8TSuaoL/concat.3.0.bcf /tmp/ZuB8TSuaoL/concat.3.c.bcf /tmp/ZuB8TSuaoL/concat.3.d.bcf /tmp/ZuB8TSuaoL/concat.3.e.bcf /tmp/ZuB8TSuaoL/concat.3.f.bcf [W::bcf_record_check] Bad BCF record: Invalid INFO id -14336 [W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080 [E::vcf_format] Invalid BCF, the FORMAT tag id=-13056 not present in the header The outputs differ: /<>/test/concat.3.bcf.out /<>/test/concat.3.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/ZuB8TSuaoL/concat.3.a.bcf /tmp/ZuB8TSuaoL/concat.3.b.bcf /tmp/ZuB8TSuaoL/concat.3.0.bcf /tmp/ZuB8TSuaoL/concat.3.c.bcf /tmp/ZuB8TSuaoL/concat.3.d.bcf /tmp/ZuB8TSuaoL/concat.3.e.bcf /tmp/ZuB8TSuaoL/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ [W::bcf_record_check] Bad BCF record: Invalid INFO id -14336 [W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080 [W::bcf_record_check] Bad BCF record: Invalid FORMAT id -13056 Random seed for test_naive_concat: 4119100768 The outputs differ: /<>/test/concat.3.bcf.out /<>/test/concat.3.bcf.out.new .. failed ... test_naive_concat: /<>/bcftools concat --naive /tmp/ZuB8TSuaoL/naive_concat.0.bcf /tmp/ZuB8TSuaoL/naive_concat.1.bcf /tmp/ZuB8TSuaoL/naive_concat.2.bcf /tmp/ZuB8TSuaoL/naive_concat.3.bcf /tmp/ZuB8TSuaoL/naive_concat.4.bcf /tmp/ZuB8TSuaoL/naive_concat.5.bcf /tmp/ZuB8TSuaoL/naive_concat.6.bcf /tmp/ZuB8TSuaoL/naive_concat.7.bcf /tmp/ZuB8TSuaoL/naive_concat.8.bcf /tmp/ZuB8TSuaoL/naive_concat.9.bcf | /<>/bcftools view -H [E::hts_realloc_or_die] Cannot allocate memory Failed to open -: unknown file type Non-zero status 255 .. failed ... test_naive_concat: /<>/bcftools concat --naive /tmp/ZuB8TSuaoL/naive_concat.0.vcf.gz /tmp/ZuB8TSuaoL/naive_concat.1.vcf.gz /tmp/ZuB8TSuaoL/naive_concat.2.vcf.gz /tmp/ZuB8TSuaoL/naive_concat.3.vcf.gz /tmp/ZuB8TSuaoL/naive_concat.4.vcf.gz /tmp/ZuB8TSuaoL/naive_concat.5.vcf.gz /tmp/ZuB8TSuaoL/naive_concat.6.vcf.gz /tmp/ZuB8TSuaoL/naive_concat.7.vcf.gz /tmp/ZuB8TSuaoL/naive_concat.8.vcf.gz /tmp/ZuB8TSuaoL/naive_concat.9.vcf.gz | /<>/bcftools view -H The outputs differ: /<>/test/concat.naive.vcf.out /<>/test/concat.naive.vcf.out.new .. failed ... test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/ZuB8TSuaoL/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZuB8TSuaoL/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/ZuB8TSuaoL/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZuB8TSuaoL/reheader.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/ZuB8TSuaoL/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZuB8TSuaoL/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/ZuB8TSuaoL/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZuB8TSuaoL/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/ZuB8TSuaoL/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZuB8TSuaoL/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/ZuB8TSuaoL/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZuB8TSuaoL/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/ZuB8TSuaoL/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZuB8TSuaoL/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/ZuB8TSuaoL/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZuB8TSuaoL/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/ZuB8TSuaoL/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZuB8TSuaoL/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/ZuB8TSuaoL/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZuB8TSuaoL/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /<>/test/empty.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/empty.vcf | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /tmp/ZuB8TSuaoL/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZuB8TSuaoL/empty.bcf | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /tmp/ZuB8TSuaoL/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZuB8TSuaoL/empty.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/ZuB8TSuaoL/rename.map -Ov /tmp/ZuB8TSuaoL/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/ZuB8TSuaoL/rename.map -Ob /tmp/ZuB8TSuaoL/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/ZuB8TSuaoL/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/ZuB8TSuaoL/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/ZuB8TSuaoL/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/convert.vcf.gz | /<>/bcftools convert -g -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/ZuB8TSuaoL/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/convert.vcf.gz | /<>/bcftools convert -g .,- 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/ZuB8TSuaoL/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/ZuB8TSuaoL/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/ZuB8TSuaoL/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/ZuB8TSuaoL/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/ZuB8TSuaoL/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/check.vcf.gz | /<>/bcftools convert -g -,. --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/ZuB8TSuaoL/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/check.vcf.gz | /<>/bcftools convert -g .,- --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/ZuB8TSuaoL/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/ZuB8TSuaoL/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/ZuB8TSuaoL/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/convert.vcf.gz | /<>/bcftools convert -h -,.,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/ZuB8TSuaoL/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/convert.vcf.gz | /<>/bcftools convert -h .,-,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/ZuB8TSuaoL/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/convert.vcf.gz | /<>/bcftools convert -h .,.,- 2>/dev/null .. ok test_vcf_convert_hls2vcf: /<>/bcftools convert -H /<>/test/convert.hls.gt.hap,/<>/test/convert.hls.gt.legend,/<>/test/convert.hls.gt.samples 2>/dev/null | grep -v ^## The outputs differ: /<>/test/convert.gt.noHead.vcf /<>/test/convert.gt.noHead.vcf.new .. failed ... test_vcf_convert_hls2vcf: /<>/bcftools convert -H /<>/test/convert.hls.gt.hap,/<>/test/convert.hls.gt.legend,/<>/test/convert.hls.gt.samples -Ou 2>/dev/null | /<>/bcftools view | grep -v ^## The outputs differ: /<>/test/convert.gt.noHead.vcf /<>/test/convert.gt.noHead.vcf.new .. failed ... test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples 2>/dev/null | grep -v ^## The outputs differ: /<>/test/convert.gt.noHead.vcf /<>/test/convert.gt.noHead.vcf.new .. failed ... test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples -Ou 2>/dev/null | /<>/bcftools view | grep -v ^## The outputs differ: /<>/test/convert.gt.noHead.vcf /<>/test/convert.gt.noHead.vcf.new .. failed ... test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/ZuB8TSuaoL/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/convert.vcf.gz | /<>/bcftools convert --hapsample -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/ZuB8TSuaoL/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/convert.vcf.gz | /<>/bcftools convert --hapsample .,- 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools convert --no-version --gvcf2vcf -f /<>/test/gvcf.fa /tmp/ZuB8TSuaoL/convert.gvcf.vcf.gz 2>/dev/null The outputs differ: /<>/test/convert.gvcf.out /<>/test/convert.gvcf.out.new .. failed ... test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/ZuB8TSuaoL/convert.gvcf.vcf.gz | /<>/bcftools convert --gvcf2vcf -f /<>/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools The outputs differ: /<>/test/convert.gvcf.out /<>/test/convert.gvcf.out.new .. failed ... test_vcf_convert_tsv2vcf: /<>/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.23andme 2>/dev/null .. ok test_vcf_convert_tsv2vcf: /<>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.23andme 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZuB8TSuaoL/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/ZuB8TSuaoL/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/ZuB8TSuaoL/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/ZuB8TSuaoL/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZuB8TSuaoL/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/ZuB8TSuaoL/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/ZuB8TSuaoL/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/ZuB8TSuaoL/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZuB8TSuaoL/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/ZuB8TSuaoL/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab -c /tmp/ZuB8TSuaoL/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/ZuB8TSuaoL/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZuB8TSuaoL/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/ZuB8TSuaoL/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/ZuB8TSuaoL/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/ZuB8TSuaoL/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZuB8TSuaoL/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZuB8TSuaoL/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZuB8TSuaoL/empty.vcf.gz -f /<>/test/consensus.fa 2>/dev/null .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -b /tmp/ZuB8TSuaoL/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/ZuB8TSuaoL/mpileup.bam.urllist 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -b /tmp/ZuB8TSuaoL/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/ZuB8TSuaoL/mpileup.cram.urllist 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa /<>/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa -Ob /<>/test/mpileup/indel-AD.1.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa /<>/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa -Ob /<>/test/mpileup/indel-AD.1.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /<>/bcftools csq -f /<>/test/csq.fa -g /<>/test/csq.gff3 /<>/test/csq.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq.gff3 ... Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs Calling... The outputs differ: /<>/test/csq.1.out /<>/test/csq.1.out.new .. failed ... test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000542803/ENST00000542803.fa -g /<>/test/csq/ENST00000542803/ENST00000542803.gff /<>/test/csq/ENST00000542803/splice-region.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000542803/ENST00000542803.gff ... Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000542803/ENST00000542803.fa -g /<>/test/csq/ENST00000542803/ENST00000542803.gff /<>/test/csq/ENST00000542803/splice-region.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000542803/ENST00000542803.gff ... Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000593942/ENST00000593942.fa -g /<>/test/csq/ENST00000593942/ENST00000593942.gff /<>/test/csq/ENST00000593942/last-codon-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000593942/ENST00000593942.gff ... Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000520868/ENST00000520868.fa -g /<>/test/csq/ENST00000520868/ENST00000520868.gff /<>/test/csq/ENST00000520868/long-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000520868/ENST00000520868.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000373833/ENST00000373833.fa -g /<>/test/csq/ENST00000373833/ENST00000373833.gff /<>/test/csq/ENST00000373833/boundary-insertion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000373833/ENST00000373833.gff ... Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000373833/ENST00000373833.fa -g /<>/test/csq/ENST00000373833/ENST00000373833.gff /<>/test/csq/ENST00000373833/boundary-insertion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000373833/ENST00000373833.gff ... Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000536784/ENST00000536784.fa -g /<>/test/csq/ENST00000536784/ENST00000536784.gff /<>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000536784/ENST00000536784.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000536784/ENST00000536784.fa -g /<>/test/csq/ENST00000536784/ENST00000536784.gff /<>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000536784/ENST00000536784.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000410009/ENST00000410009.fa -g /<>/test/csq/ENST00000410009/ENST00000410009.gff /<>/test/csq/ENST00000410009/frameshift.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000410009/ENST00000410009.gff ... Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs Calling... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String The outputs differ: /<>/test/csq/ENST00000410009/frameshift.txt /<>/test/csq/ENST00000410009/frameshift.txt.new .. failed ... test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENSG00000173376/ENSG00000173376.fa -g /<>/test/csq/ENSG00000173376/ENSG00000173376.gff /<>/test/csq/ENSG00000173376/synon.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENSG00000173376/ENSG00000173376.gff ... Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000375992/ENST00000375992.fa -g /<>/test/csq/ENST00000375992/ENST00000375992.gff /<>/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000375992/ENST00000375992.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... The outputs differ: /<>/test/csq/ENST00000341065/frame1.txt /<>/test/csq/ENST00000341065/frame1.txt.new .. failed ... test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... The outputs differ: /<>/test/csq/ENST00000341065/frame1.txt-l /<>/test/csq/ENST00000341065/frame1.txt-l.new .. failed ... test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String The outputs differ: /<>/test/csq/ENST00000341065/frame2.txt /<>/test/csq/ENST00000341065/frame2.txt.new .. failed ... test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... [E::vcf_format] Invalid BCF, the INFO index is too large The outputs differ: /<>/test/csq/ENST00000341065/frame2.txt-l /<>/test/csq/ENST00000341065/frame2.txt-l.new .. failed ... test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String The outputs differ: /<>/test/csq/ENST00000341065/frame3.txt /<>/test/csq/ENST00000341065/frame3.txt.new .. failed ... test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String The outputs differ: /<>/test/csq/ENST00000341065/frame3.txt-l /<>/test/csq/ENST00000341065/frame3.txt-l.new .. failed ... test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000519442/ENST00000519442.fa -g /<>/test/csq/ENST00000519442/ENST00000519442.gff /<>/test/csq/ENST00000519442/synon-splice-region-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000519442/ENST00000519442.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000413103/ENST00000413103.fa -g /<>/test/csq/ENST00000413103/ENST00000413103.gff /<>/test/csq/ENST00000413103/long-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000413103/ENST00000413103.gff ... Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000294661/ENST00000294661.fa -g /<>/test/csq/ENST00000294661/ENST00000294661.gff /<>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000294661/ENST00000294661.fa -g /<>/test/csq/ENST00000294661/ENST00000294661.gff /<>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000557788/ENST00000557788.fa -g /<>/test/csq/ENST00000557788/ENST00000557788.gff /<>/test/csq/ENST00000557788/long-overlap-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000557788/ENST00000557788.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000382647/ENST00000382647.fa -g /<>/test/csq/ENST00000382647/ENST00000382647.gff /<>/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000382647/ENST00000382647.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000318249/ENST00000318249.fa -g /<>/test/csq/ENST00000318249/ENST00000318249.gff /<>/test/csq/ENST00000318249/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000318249/ENST00000318249.gff ... Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000318249/ENST00000318249.fa -g /<>/test/csq/ENST00000318249/ENST00000318249.gff /<>/test/csq/ENST00000318249/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000318249/ENST00000318249.gff ... Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000301246/ENST00000301246.fa -g /<>/test/csq/ENST00000301246/ENST00000301246.gff /<>/test/csq/ENST00000301246/15bp-insert.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000301246/ENST00000301246.gff ... Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs Calling... [E::vcf_format] Invalid BCF, the INFO index is too large The outputs differ: /<>/test/csq/ENST00000301246/15bp-insert.txt /<>/test/csq/ENST00000301246/15bp-insert.txt.new .. failed ... test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000303039/ENST00000303039.fa -g /<>/test/csq/ENST00000303039/ENST00000303039.gff /<>/test/csq/ENST00000303039/not-a-stop.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000303039/ENST00000303039.fa -g /<>/test/csq/ENST00000303039/ENST00000303039.gff /<>/test/csq/ENST00000303039/not-a-stop.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000448695/ENST00000448695.fa -g /<>/test/csq/ENST00000448695/ENST00000448695.gff /<>/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000448695/ENST00000448695.gff ... Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000528237/ENST00000528237.fa -g /<>/test/csq/ENST00000528237/ENST00000528237.gff /<>/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000528237/ENST00000528237.gff ... Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000624631/ENST00000624631.fa -g /<>/test/csq/ENST00000624631/ENST00000624631.gff /<>/test/csq/ENST00000624631/ambiguous.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000624631/ENST00000624631.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... /bin/bash: line 1: 7148 Done /<>/bcftools csq -f /<>/test/csq/ENST00000624631/ENST00000624631.fa -g /<>/test/csq/ENST00000624631/ENST00000624631.gff /<>/test/csq/ENST00000624631/ambiguous.vcf 7149 | /<>/test/csq/sort-csq 7150 Segmentation fault (core dumped) | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Non-zero status 139 .. failed ... test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000378322/ENST00000378322.fa -g /<>/test/csq/ENST00000378322/ENST00000378322.gff /<>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000378322/ENST00000378322.fa -g /<>/test/csq/ENST00000378322/ENST00000378322.gff /<>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000357367/ENST00000357367.fa -g /<>/test/csq/ENST00000357367/ENST00000357367.gff /<>/test/csq/ENST00000357367/stop-retained.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000357367/ENST00000357367.gff ... Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000543077/ENST00000543077.fa -g /<>/test/csq/ENST00000543077/ENST00000543077.gff /<>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000543077/ENST00000543077.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000543077/ENST00000543077.fa -g /<>/test/csq/ENST00000543077/ENST00000543077.gff /<>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000543077/ENST00000543077.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/snps.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/snps.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/insert3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/insert3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000256452/ENST00000256452.fa -g /<>/test/csq/ENST00000256452/ENST00000256452.gff /<>/test/csq/ENST00000256452/intron.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000256452/ENST00000256452.gff ... Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000420670/ENST00000420670.fa -g /<>/test/csq/ENST00000420670/ENST00000420670.gff /<>/test/csq/ENST00000420670/start-stop-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000420670/ENST00000420670.gff ... Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000409523/ENST00000409523.fa -g /<>/test/csq/ENST00000409523/ENST00000409523.gff /<>/test/csq/ENST00000409523/long-overlapping-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000409523/ENST00000409523.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000295641/ENST00000295641.fa -g /<>/test/csq/ENST00000295641/ENST00000295641.gff /<>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000295641/ENST00000295641.gff ... Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000295641/ENST00000295641.fa -g /<>/test/csq/ENST00000295641/ENST00000295641.gff /<>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000295641/ENST00000295641.gff ... Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000271583/ENST00000271583.fa -g /<>/test/csq/ENST00000271583/ENST00000271583.gff /<>/test/csq/ENST00000271583/splice-acceptor.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000271583/ENST00000271583.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000479739/ENST00000479739.fa -g /<>/test/csq/ENST00000479739/ENST00000479739.gff /<>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000479739/ENST00000479739.gff ... Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000479739/ENST00000479739.fa -g /<>/test/csq/ENST00000479739/ENST00000479739.gff /<>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000479739/ENST00000479739.gff ... Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000545279/ENST00000545279.fa -g /<>/test/csq/ENST00000545279/ENST00000545279.gff /<>/test/csq/ENST00000545279/splice-region-insert.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000545279/ENST00000545279.gff ... Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000227471/ENST00000227471.fa -g /<>/test/csq/ENST00000227471/ENST00000227471.gff /<>/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000227471/ENST00000227471.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000218032/ENST00000218032.fa -g /<>/test/csq/ENST00000218032/ENST00000218032.gff /<>/test/csq/ENST00000218032/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000218032/ENST00000218032.fa -g /<>/test/csq/ENST00000218032/ENST00000218032.gff /<>/test/csq/ENST00000218032/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000368801/ENST00000368801.fa -g /<>/test/csq/ENST00000368801/ENST00000368801.gff /<>/test/csq/ENST00000368801/compound-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000368801/ENST00000368801.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs Calling... [E::vcf_format] Invalid BCF, the INFO index is too large The outputs differ: /<>/test/csq/ENST00000368801/compound-lost.txt /<>/test/csq/ENST00000368801/compound-lost.txt.new .. failed ... test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000436063/ENST00000436063.fa -g /<>/test/csq/ENST00000436063/ENST00000436063.gff /<>/test/csq/ENST00000436063/insert-before-utr.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000436063/ENST00000436063.gff ... Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000381157/ENST00000381157.fa -g /<>/test/csq/ENST00000381157/ENST00000381157.gff /<>/test/csq/ENST00000381157/haploid-diploid.vcf | /<>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' Parsing /<>/test/csq/ENST00000381157/ENST00000381157.gff ... Indexed 1 transcripts, 6 exons, 6 CDSs, 0 UTRs Calling... Warning: Skipping site with non-diploid/non-haploid genotypes at X:31180 C>T The outputs differ: /<>/test/csq/ENST00000381157/haploid-diploid.txt /<>/test/csq/ENST00000381157/haploid-diploid.txt.new .. failed ... test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000573314/ENST00000573314.fa -g /<>/test/csq/ENST00000573314/ENST00000573314.gff /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000573314/ENST00000573314.gff ... Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs Calling... [E::vcf_format] Invalid BCF, the INFO index is too large The outputs differ: /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt.new .. failed ... test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000573314/ENST00000573314.fa -g /<>/test/csq/ENST00000573314/ENST00000573314.gff /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000573314/ENST00000573314.gff ... Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs Calling... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String The outputs differ: /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l.new .. failed ... test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000329454/ENST00000329454.fa -g /<>/test/csq/ENST00000329454/ENST00000329454.gff /<>/test/csq/ENST00000329454/boundary-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000329454/ENST00000329454.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000329454/ENST00000329454.fa -g /<>/test/csq/ENST00000329454/ENST00000329454.gff /<>/test/csq/ENST00000329454/boundary-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000329454/ENST00000329454.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000520795/ENST00000520795.fa -g /<>/test/csq/ENST00000520795/ENST00000520795.gff /<>/test/csq/ENST00000520795/long-inside-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000520795/ENST00000520795.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000520795/ENST00000520795.fa -g /<>/test/csq/ENST00000520795/ENST00000520795.gff /<>/test/csq/ENST00000520795/long-inside-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000520795/ENST00000520795.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000390520/ENST00000390520.fa -g /<>/test/csq/ENST00000390520/ENST00000390520.gff /<>/test/csq/ENST00000390520/deletion-overlap.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000390520/ENST00000390520.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs Calling... .. ok Number of tests: total .. 793 passed .. 672 failed .. 121 Makefile:246: recipe for target 'test-plugins' failed make[1]: *** [test-plugins] Error 1 make[1]: Leaving directory '/<>' dh_auto_test: make -j4 -Oline test VERBOSE=1 returned exit code 2 debian/rules:7: recipe for target 'build-arch' failed make: *** [build-arch] Error 25 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20180504-1605 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 30188 Build-Time: 44 Distribution: cosmic Fail-Stage: build Host Architecture: s390x Install-Time: 10 Job: bcftools_1.7-2.dsc Machine Architecture: s390x Package: bcftools Package-Time: 55 Source-Version: 1.7-2 Space: 30188 Status: attempted Version: 1.7-2 -------------------------------------------------------------------------------- Finished at 20180504-1605 Build needed 00:00:55, 30188k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=cosmic --arch=s390x PACKAGEBUILD-14825711 Scanning for processes to kill in build PACKAGEBUILD-14825711 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=cosmic --arch=s390x PACKAGEBUILD-14825711 Stopping target for build PACKAGEBUILD-14825711 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=cosmic --arch=s390x PACKAGEBUILD-14825711 Removing build PACKAGEBUILD-14825711