RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-001 4.4.0-96-generic #119-Ubuntu SMP Tue Sep 12 14:59:54 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_152 python-lpbuildd_152 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_1:2.7.4-0ubuntu1.2 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 23 Sep 09:05:24 ntpdate[1804]: adjust time server 10.211.37.1 offset 0.000215 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13408087 /home/buildd/filecache-default/b6762bcd0bec7d108ffb0fb3fb0b7d1ce32df8bb Creating target for build PACKAGEBUILD-13408087 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13408087 Starting target for build PACKAGEBUILD-13408087 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13408087 'deb http://ftpmaster.internal/ubuntu artful main universe' Overriding sources.list in build-PACKAGEBUILD-13408087 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13408087 Updating target for build PACKAGEBUILD-13408087 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main i386 Packages [1077 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main Translation-en [544 kB] Get:4 http://ftpmaster.internal/ubuntu artful/universe i386 Packages [8056 kB] Get:5 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4785 kB] Fetched 14.7 MB in 3s (3730 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13408087 i386 artful -c chroot:build-PACKAGEBUILD-13408087 --arch=i386 --dist=artful --nolog bcftools_1.4.1-3build1.dsc Initiating build PACKAGEBUILD-13408087 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-96-generic #119-Ubuntu SMP Tue Sep 12 14:59:54 UTC 2017 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-001.buildd +==============================================================================+ | bcftools 1.4.1-3build1 (i386) 23 Sep 2017 09:05 | +==============================================================================+ Package: bcftools Version: 1.4.1-3build1 Source Version: 1.4.1-3build1 Distribution: artful Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/bcftools-2w1pv7/bcftools-1.4.1' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-2w1pv7' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13408087/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bcftools_1.4.1-3build1.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-XwuSdq/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-XwuSdq/apt_archive ./ InRelease Get:2 copy:/<>/resolver-XwuSdq/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-XwuSdq/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-XwuSdq/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-XwuSdq/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (248 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 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-XwuSdq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12671 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.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, libhts-dev (>= 1.3.1), libgsl-dev, tabix, libio-pty-perl Filtered Build-Depends: debhelper (>= 10), zlib1g-dev, libhts-dev (>= 1.3.1), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<>/resolver-Ke31af/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. Ign:1 copy:/<>/resolver-Ke31af/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Ke31af/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Ke31af/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Ke31af/apt_archive ./ Sources [247 B] Get:5 copy:/<>/resolver-Ke31af/apt_archive ./ Packages [565 B] Fetched 2931 B in 0s (165 kB/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 libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libhts-dev libhts2 libicu57 libio-pty-perl liblzma-dev libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* 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 libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libhts-dev libhts2 libicu57 libio-pty-perl liblzma-dev libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 39 newly installed, 1 to remove and 0 not upgraded. Need to get 19.9 MB of archives. After this operation, 76.3 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Ke31af/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [820 B] Get:2 http://ftpmaster.internal/ubuntu artful/main i386 groff-base i386 1.22.3-9 [1163 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main i386 libbsd0 i386 0.8.6-1 [45.1 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main i386 bsdmainutils i386 9.0.12+nmu1ubuntu1 [181 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main i386 libpipeline1 i386 1.4.2-1 [26.8 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main i386 man-db i386 2.7.6.1-2 [906 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main i386 libmagic-mgc i386 1:5.32-1 [184 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main i386 libmagic1 i386 1:5.32-1 [75.0 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main i386 file i386 1:5.32-1 [21.9 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main i386 gettext-base i386 0.19.8.1-4ubuntu1 [50.7 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main i386 libglib2.0-0 i386 2.54.0-1ubuntu1 [1231 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main i386 libicu57 i386 57.1-6 [7837 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main i386 libxml2 i386 2.9.4+dfsg1-3.1 [705 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main i386 libsigsegv2 i386 2.11-1 [13.5 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main i386 m4 i386 1.4.18-1 [196 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main i386 autoconf all 2.69-11 [322 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main i386 autotools-dev all 20161112.1 [39.5 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main i386 automake all 1:1.15-6ubuntu1 [509 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main i386 autopoint all 0.19.8.1-4ubuntu1 [412 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main i386 libtool all 2.4.6-2 [194 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main i386 dh-autoreconf all 14 [15.5 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main i386 libarchive-zip-perl all 1.59-1 [84.0 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main i386 libfile-stripnondeterminism-perl all 0.038-1 [13.3 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main i386 libtimedate-perl all 2.3000-2 [37.5 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main i386 dh-strip-nondeterminism all 0.038-1 [5026 B] Get:26 http://ftpmaster.internal/ubuntu artful/main i386 libcroco3 i386 0.6.12-1 [87.5 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main i386 gettext i386 0.19.8.1-4ubuntu1 [1097 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main i386 po-debconf all 1.0.20 [232 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main i386 debhelper all 10.7.2ubuntu2 [877 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main i386 libgslcblas0 i386 2.4+dfsg-6 [80.5 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main i386 libgsl23 i386 2.4+dfsg-6 [802 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main i386 libgsl-dev i386 2.4+dfsg-6 [1042 kB] Get:34 http://ftpmaster.internal/ubuntu artful/universe i386 libhts2 i386 1.5-1 [304 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main i386 liblzma-dev i386 5.2.2-1.3 [154 kB] Get:36 http://ftpmaster.internal/ubuntu artful/universe i386 tabix i386 1.5-1 [335 kB] Get:37 http://ftpmaster.internal/ubuntu artful/universe i386 libhts-dev i386 1.5-1 [411 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main i386 libio-pty-perl i386 1:1.08-1.1build4 [30.8 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main i386 zlib1g-dev i386 1:1.2.11.dfsg-0ubuntu2 [178 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.9 MB in 0s (45.0 MB/s) (Reading database ... 12671 files and directories currently installed.) Removing pkg-create-dbgsym (0.73) ... Selecting previously unselected package groff-base. (Reading database ... 12662 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_i386.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../01-libbsd0_0.8.6-1_i386.deb ... Unpacking libbsd0:i386 (0.8.6-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_9.0.12+nmu1ubuntu1_i386.deb ... Unpacking bsdmainutils (9.0.12+nmu1ubuntu1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.4.2-1_i386.deb ... Unpacking libpipeline1:i386 (1.4.2-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.7.6.1-2_i386.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.32-1_i386.deb ... Unpacking libmagic-mgc (1:5.32-1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../06-libmagic1_1%3a5.32-1_i386.deb ... Unpacking libmagic1:i386 (1:5.32-1) ... Selecting previously unselected package file. Preparing to unpack .../07-file_1%3a5.32-1_i386.deb ... Unpacking file (1:5.32-1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../08-gettext-base_0.19.8.1-4ubuntu1_i386.deb ... Unpacking gettext-base (0.19.8.1-4ubuntu1) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../09-libglib2.0-0_2.54.0-1ubuntu1_i386.deb ... Unpacking libglib2.0-0:i386 (2.54.0-1ubuntu1) ... Selecting previously unselected package libicu57:i386. Preparing to unpack .../10-libicu57_57.1-6_i386.deb ... Unpacking libicu57:i386 (57.1-6) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../11-libxml2_2.9.4+dfsg1-3.1_i386.deb ... Unpacking libxml2:i386 (2.9.4+dfsg1-3.1) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../12-libsigsegv2_2.11-1_i386.deb ... Unpacking libsigsegv2:i386 (2.11-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-1_i386.deb ... Unpacking m4 (1.4.18-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20161112.1_all.deb ... Unpacking autotools-dev (20161112.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.15-6ubuntu1_all.deb ... Unpacking automake (1:1.15-6ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.19.8.1-4ubuntu1_all.deb ... Unpacking autopoint (0.19.8.1-4ubuntu1) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-2_all.deb ... Unpacking libtool (2.4.6-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_14_all.deb ... Unpacking dh-autoreconf (14) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.59-1_all.deb ... Unpacking libarchive-zip-perl (1.59-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_0.038-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.038-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../22-libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_0.038-1_all.deb ... Unpacking dh-strip-nondeterminism (0.038-1) ... Selecting previously unselected package libcroco3:i386. Preparing to unpack .../24-libcroco3_0.6.12-1_i386.deb ... Unpacking libcroco3:i386 (0.6.12-1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.19.8.1-4ubuntu1_i386.deb ... Unpacking gettext (0.19.8.1-4ubuntu1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.20_all.deb ... Unpacking po-debconf (1.0.20) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_10.7.2ubuntu2_all.deb ... Unpacking debhelper (10.7.2ubuntu2) ... Selecting previously unselected package libgslcblas0:i386. Preparing to unpack .../29-libgslcblas0_2.4+dfsg-6_i386.deb ... Unpacking libgslcblas0:i386 (2.4+dfsg-6) ... Selecting previously unselected package libgsl23:i386. Preparing to unpack .../30-libgsl23_2.4+dfsg-6_i386.deb ... Unpacking libgsl23:i386 (2.4+dfsg-6) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../31-libgsl-dev_2.4+dfsg-6_i386.deb ... Unpacking libgsl-dev (2.4+dfsg-6) ... Selecting previously unselected package libhts2:i386. Preparing to unpack .../32-libhts2_1.5-1_i386.deb ... Unpacking libhts2:i386 (1.5-1) ... Selecting previously unselected package liblzma-dev:i386. Preparing to unpack .../33-liblzma-dev_5.2.2-1.3_i386.deb ... Unpacking liblzma-dev:i386 (5.2.2-1.3) ... Selecting previously unselected package tabix. Preparing to unpack .../34-tabix_1.5-1_i386.deb ... Unpacking tabix (1.5-1) ... Selecting previously unselected package libhts-dev:i386. Preparing to unpack .../35-libhts-dev_1.5-1_i386.deb ... Unpacking libhts-dev:i386 (1.5-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../36-libio-pty-perl_1%3a1.08-1.1build4_i386.deb ... Unpacking libio-pty-perl (1:1.08-1.1build4) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../37-zlib1g-dev_1%3a1.2.11.dfsg-0ubuntu2_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.11.dfsg-0ubuntu2) ... Selecting previously unselected package sbuild-build-depends-bcftools-dummy. Preparing to unpack .../38-sbuild-build-depends-bcftools-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libio-pty-perl (1:1.08-1.1build4) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:i386 (2.11-1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:i386 (2.54.0-1ubuntu1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-4ubuntu1) ... Setting up libpipeline1:i386 (1.4.2-1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:i386 (57.1-6) ... Setting up libbsd0:i386 (0.8.6-1) ... Setting up libxml2:i386 (2.9.4+dfsg1-3.1) ... Setting up libmagic-mgc (1:5.32-1) ... Setting up libmagic1:i386 (1:5.32-1) ... Setting up libcroco3:i386 (0.6.12-1) ... Processing triggers for libc-bin (2.26-0ubuntu1) ... Setting up autotools-dev (20161112.1) ... Setting up tabix (1.5-1) ... Setting up liblzma-dev:i386 (5.2.2-1.3) ... Setting up bsdmainutils (9.0.12+nmu1ubuntu1) ... 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:i386 (2.4+dfsg-6) ... Setting up libhts2:i386 (1.5-1) ... Setting up autopoint (0.19.8.1-4ubuntu1) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.038-1) ... Setting up libgsl23:i386 (2.4+dfsg-6) ... Setting up gettext (0.19.8.1-4ubuntu1) ... Setting up libgsl-dev (2.4+dfsg-6) ... Setting up libhts-dev:i386 (1.5-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.038-1) ... Setting up debhelper (10.7.2ubuntu2) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... (Reading database ... 14923 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.26-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-96-generic amd64 (i686) Toolchain package versions: binutils_2.29.1-1ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-7_7.2.0-6ubuntu1 gcc-7_7.2.0-6ubuntu1 libc6-dev_2.26-0ubuntu1 libstdc++-7-dev_7.2.0-6ubuntu1 libstdc++6_7.2.0-6ubuntu1 linux-libc-dev_4.13.0-11.12 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.5~rc4 apt-transport-https_1.5~rc4 autoconf_2.69-11 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-4ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu101 base-passwd_3.5.43 bash_4.4-5ubuntu1 binutils_2.29.1-1ubuntu1 binutils-common_2.29.1-1ubuntu1 binutils-i686-linux-gnu_2.29.1-1ubuntu1 bsdmainutils_9.0.12+nmu1ubuntu1 bsdutils_1:2.30.1-0ubuntu4 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20170717 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sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tabix_1.5-1 tar_1.29b-2 tzdata_2017b-2 ubuntu-keyring_2016.10.27 util-linux_2.30.1-0ubuntu4 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 Sun Aug 6 00:25:26 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.4.1-3build1.dsc dpkg-source: info: extracting bcftools in bcftools-1.4.1 dpkg-source: info: unpacking bcftools_1.4.1.orig.tar.gz dpkg-source: info: unpacking bcftools_1.4.1-3build1.debian.tar.xz dpkg-source: info: applying external-libs.patch dpkg-source: info: applying compiler-flags.patch dpkg-source: info: applying destdir.patch dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying test-regidx-unsigned-char.patch dpkg-source: info: applying fix-bufffer-overflow.patch dpkg-source: info: applying fix-test_vcf_query.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym 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-13408087 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13408087 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13408087 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 1.4.1-3build1 dpkg-buildpackage: info: source distribution artful dpkg-source --before-build bcftools-1.4.1 dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --parallel dh_auto_clean make -j4 distclean make[1]: Entering directory '/<>' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f gmon.out *.o *~ bcftools version.h plugins/*.so plugins/*.P rm -rf *.dSYM plugins/*.dSYM test/*.dSYM rm -f TAGS make[1]: Leaving directory '/<>' dh_autoreconf_clean dh_clean debian/rules build-arch dh build-arch --parallel dh_update_autotools_config -a -O--parallel dh_autoreconf -a -O--parallel dh_auto_configure -a -O--parallel dh_auto_build -a -O--parallel make -j4 make[1]: Entering directory '/<>' echo '#define BCFTOOLS_VERSION "1.4.1"' > version.h cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfplugin.o vcfplugin.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polysomy.o polysomy.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o peakfit.o peakfit.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -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 -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -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 -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixploidy.so ploidy.c version.c plugins/fixploidy.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -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 -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -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 -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -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 -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/isecGT.so version.c plugins/isecGT.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -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 -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c cc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lm -lz -ldl -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lm -lz -ldl -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -rdynamic -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 mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o ccall.o em.o prob1.o kmin.o polysomy.o peakfit.o -lpthread -lgsl -lgslcblas -lm -lz -ldl -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts make[1]: Leaving directory '/<>' dh_auto_test -a -O--parallel make -j4 test make[1]: Entering directory '/<>' ./test/test-regidx ./test/test.pl --exec bgzip=/usr/bin/bgzip --exec tabix=/usr/bin/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 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 polysomy .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: /usr/bin/tabix /tmp/dzlw_Yss_E/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/dzlw_Yss_E/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: /usr/bin/tabix /tmp/dzlw_Yss_E/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/dzlw_Yss_E/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/dzlw_Yss_E/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/dzlw_Yss_E/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/dzlw_Yss_E/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/dzlw_Yss_E/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/dzlw_Yss_E/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/dzlw_Yss_E/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/dzlw_Yss_E/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/dzlw_Yss_E/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/dzlw_Yss_E/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/dzlw_Yss_E/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/dzlw_Yss_E/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/dzlw_Yss_E/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/dzlw_Yss_E/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/dzlw_Yss_E/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/dzlw_Yss_E/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/dzlw_Yss_E/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/dzlw_Yss_E/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/dzlw_Yss_E/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/dzlw_Yss_E/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/dzlw_Yss_E/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/dzlw_Yss_E/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/dzlw_Yss_E/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/dzlw_Yss_E/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/check.1.chk /tmp/dzlw_Yss_E/check.2.chk /tmp/dzlw_Yss_E/check.3.chk /tmp/dzlw_Yss_E/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/dzlw_Yss_E/stats.a.vcf.gz /tmp/dzlw_Yss_E/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/dzlw_Yss_E/stats.a.vcf.gz /tmp/dzlw_Yss_E/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/dzlw_Yss_E/isec.a.vcf.gz /tmp/dzlw_Yss_E/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/dzlw_Yss_E/isec.a.vcf.gz /tmp/dzlw_Yss_E/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/dzlw_Yss_E/isec.a.vcf.gz /tmp/dzlw_Yss_E/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/dzlw_Yss_E/isec.a.vcf.gz /tmp/dzlw_Yss_E/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/dzlw_Yss_E/isec.a.vcf.gz /tmp/dzlw_Yss_E/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/dzlw_Yss_E/isec.a.vcf.gz /tmp/dzlw_Yss_E/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/dzlw_Yss_E/isec.a.vcf.gz /tmp/dzlw_Yss_E/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/dzlw_Yss_E/isec.a.vcf.gz /tmp/dzlw_Yss_E/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/dzlw_Yss_E/isec.a.vcf.gz /tmp/dzlw_Yss_E/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/dzlw_Yss_E/isec.a.vcf.gz /tmp/dzlw_Yss_E/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/dzlw_Yss_E/isec.tab.gz /tmp/dzlw_Yss_E/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/dzlw_Yss_E/isec.tab.gz /tmp/dzlw_Yss_E/isec.a.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/dzlw_Yss_E/merge.a.vcf.gz /tmp/dzlw_Yss_E/merge.b.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.a.vcf.gz /tmp/dzlw_Yss_E/merge.b.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.a.vcf.gz /tmp/dzlw_Yss_E/merge.b.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.a.vcf.gz /tmp/dzlw_Yss_E/merge.b.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.a.vcf.gz /tmp/dzlw_Yss_E/merge.b.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.a.vcf.gz /tmp/dzlw_Yss_E/merge.b.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.2.a.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.2.a.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.2.a.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.2.a.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.2.a.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.2.a.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.3.a.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.3.a.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.4.a.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.4.a.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/gvcf.merge.1.vcf.gz /tmp/dzlw_Yss_E/gvcf.merge.2.vcf.gz /tmp/dzlw_Yss_E/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/dzlw_Yss_E/gvcf.merge.1.vcf.gz /tmp/dzlw_Yss_E/gvcf.merge.2.vcf.gz /tmp/dzlw_Yss_E/gvcf.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/dzlw_Yss_E/merge.gvcf.2.a.vcf.gz /tmp/dzlw_Yss_E/merge.gvcf.2.b.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/merge.gvcf.2.a.vcf.gz /tmp/dzlw_Yss_E/merge.gvcf.2.b.vcf.gz /tmp/dzlw_Yss_E/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 /tmp/dzlw_Yss_E/merge.5.a.vcf.gz /tmp/dzlw_Yss_E/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/dzlw_Yss_E/merge.5.a.vcf.gz /tmp/dzlw_Yss_E/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/dzlw_Yss_E/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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"' /tmp/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' /tmp/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' .. ok test_vcf_query: /<>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' /tmp/dzlw_Yss_E/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' /tmp/dzlw_Yss_E/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/query.filter.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' /tmp/dzlw_Yss_E/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/query.filter.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' /tmp/dzlw_Yss_E/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/query.filter.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' /tmp/dzlw_Yss_E/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/query.filter.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/dzlw_Yss_E/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/missing.vcf.gz | /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/dzlw_Yss_E/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/dzlw_Yss_E/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/query.filter.2.vcf.gz | /<>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx -f /<>/test/norm.fa /tmp/dzlw_Yss_E/norm.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -cx -f /<>/test/norm.fa /tmp/dzlw_Yss_E/norm.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/dzlw_Yss_E/norm.split.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.split.out /<>/test/norm.split.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/dzlw_Yss_E/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.split.out /<>/test/norm.split.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/dzlw_Yss_E/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/dzlw_Yss_E/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/dzlw_Yss_E/norm.split.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.split.and.norm.out /<>/test/norm.split.and.norm.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m- -f /<>/test/norm.fa /tmp/dzlw_Yss_E/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.split.and.norm.out /<>/test/norm.split.and.norm.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/dzlw_Yss_E/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/dzlw_Yss_E/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.merge.out /<>/test/norm.merge.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/dzlw_Yss_E/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/dzlw_Yss_E/norm.merge.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/dzlw_Yss_E/norm.merge.3.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.merge.3.out /<>/test/norm.merge.3.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/dzlw_Yss_E/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 '.' The outputs differ: /<>/test/norm.merge.3.out /<>/test/norm.merge.3.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/dzlw_Yss_E/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/dzlw_Yss_E/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ 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/dzlw_Yss_E/norm.setref.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/dzlw_Yss_E/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/dzlw_Yss_E/norm.telomere.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/dzlw_Yss_E/norm.telomere.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/dzlw_Yss_E/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/dzlw_Yss_E/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/dzlw_Yss_E/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/dzlw_Yss_E/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/dzlw_Yss_E/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/dzlw_Yss_E/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/dzlw_Yss_E/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/dzlw_Yss_E/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/dzlw_Yss_E/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/dzlw_Yss_E/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/dzlw_Yss_E/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/dzlw_Yss_E/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/dzlw_Yss_E/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/dzlw_Yss_E/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/dzlw_Yss_E/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/dzlw_Yss_E/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/dzlw_Yss_E/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/dzlw_Yss_E/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/dzlw_Yss_E/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/dzlw_Yss_E/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/dzlw_Yss_E/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/dzlw_Yss_E/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/dzlw_Yss_E/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/dzlw_Yss_E/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/dzlw_Yss_E/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/dzlw_Yss_E/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/dzlw_Yss_E/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/dzlw_Yss_E/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/dzlw_Yss_E/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/dzlw_Yss_E/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/dzlw_Yss_E/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/dzlw_Yss_E/view.vectors.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/dzlw_Yss_E/view.vectors.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[0]="AAAAAA"' /tmp/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[2]="C"' /tmp/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[4]="EE"' /tmp/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[1]="BB"' /tmp/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/dzlw_Yss_E/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/dzlw_Yss_E/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/dzlw_Yss_E/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/dzlw_Yss_E/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/dzlw_Yss_E/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/dzlw_Yss_E/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/dzlw_Yss_E/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/dzlw_Yss_E/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/dzlw_Yss_E/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/dzlw_Yss_E/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/dzlw_Yss_E/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 .. ok test_vcf_call: /<>/bcftools call -Ob -mg0 /<>/test/mpileup.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.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/dzlw_Yss_E/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/dzlw_Yss_E/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_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -mx -g2 -G2 /<>/test/filter.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok 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_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab /tmp/dzlw_Yss_E/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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/dzlw_Yss_E/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/dzlw_Yss_E/regions.tab.gz /tmp/dzlw_Yss_E/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/dzlw_Yss_E/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/dzlw_Yss_E/regions.tab.gz /tmp/dzlw_Yss_E/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/dzlw_Yss_E/regions.bed /tmp/dzlw_Yss_E/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/dzlw_Yss_E/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/dzlw_Yss_E/regions.bed /tmp/dzlw_Yss_E/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/dzlw_Yss_E/regions.bed.gz /tmp/dzlw_Yss_E/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/dzlw_Yss_E/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/dzlw_Yss_E/regions.bed.gz /tmp/dzlw_Yss_E/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/dzlw_Yss_E/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/dzlw_Yss_E/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/dzlw_Yss_E/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/dzlw_Yss_E/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/dzlw_Yss_E/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/dzlw_Yss_E/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/dzlw_Yss_E/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/dzlw_Yss_E/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/dzlw_Yss_E/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/dzlw_Yss_E/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate4.out /<>/test/annotate4.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/dzlw_Yss_E/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/dzlw_Yss_E/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate4.out /<>/test/annotate4.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/dzlw_Yss_E/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/dzlw_Yss_E/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/dzlw_Yss_E/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/dzlw_Yss_E/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/dzlw_Yss_E/annots4.vcf.gz -c +INFO /tmp/dzlw_Yss_E/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate8.out /<>/test/annotate8.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/dzlw_Yss_E/annots4.vcf.gz -c +INFO /tmp/dzlw_Yss_E/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate8.out /<>/test/annotate8.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/dzlw_Yss_E/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_ The outputs differ: /<>/test/annotate8.out /<>/test/annotate8.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/dzlw_Yss_E/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_ The outputs differ: /<>/test/annotate8.out /<>/test/annotate8.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/dzlw_Yss_E/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_ The outputs differ: /<>/test/annotate10.out /<>/test/annotate10.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/dzlw_Yss_E/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_ The outputs differ: /<>/test/annotate10.out /<>/test/annotate10.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/dzlw_Yss_E/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/dzlw_Yss_E/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate11.out /<>/test/annotate11.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/dzlw_Yss_E/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/dzlw_Yss_E/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate11.out /<>/test/annotate11.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/dzlw_Yss_E/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_ The outputs differ: /<>/test/annotate11.out /<>/test/annotate11.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/dzlw_Yss_E/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_ The outputs differ: /<>/test/annotate11.out /<>/test/annotate11.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/dzlw_Yss_E/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/dzlw_Yss_E/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/dzlw_Yss_E/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/dzlw_Yss_E/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/dzlw_Yss_E/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/dzlw_Yss_E/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/dzlw_Yss_E/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/dzlw_Yss_E/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/dzlw_Yss_E/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/dzlw_Yss_E/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/dzlw_Yss_E/concat.1.a.vcf.gz /tmp/dzlw_Yss_E/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/dzlw_Yss_E/concat.1.a.vcf.gz /tmp/dzlw_Yss_E/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/dzlw_Yss_E/concat.1.a.bcf /tmp/dzlw_Yss_E/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/dzlw_Yss_E/concat.1.a.bcf /tmp/dzlw_Yss_E/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/dzlw_Yss_E/concat.2.a.vcf.gz /tmp/dzlw_Yss_E/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/dzlw_Yss_E/concat.2.a.vcf.gz /tmp/dzlw_Yss_E/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/dzlw_Yss_E/concat.2.a.bcf /tmp/dzlw_Yss_E/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/dzlw_Yss_E/concat.2.a.bcf /tmp/dzlw_Yss_E/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/dzlw_Yss_E/concat.2.a.vcf.gz /tmp/dzlw_Yss_E/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/dzlw_Yss_E/concat.2.a.vcf.gz /tmp/dzlw_Yss_E/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/dzlw_Yss_E/concat.2.a.bcf /tmp/dzlw_Yss_E/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/dzlw_Yss_E/concat.2.a.bcf /tmp/dzlw_Yss_E/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/dzlw_Yss_E/concat.3.a.vcf.gz /tmp/dzlw_Yss_E/concat.3.b.vcf.gz /tmp/dzlw_Yss_E/concat.3.0.vcf.gz /tmp/dzlw_Yss_E/concat.3.c.vcf.gz /tmp/dzlw_Yss_E/concat.3.d.vcf.gz /tmp/dzlw_Yss_E/concat.3.e.vcf.gz /tmp/dzlw_Yss_E/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/dzlw_Yss_E/concat.3.a.vcf.gz /tmp/dzlw_Yss_E/concat.3.b.vcf.gz /tmp/dzlw_Yss_E/concat.3.0.vcf.gz /tmp/dzlw_Yss_E/concat.3.c.vcf.gz /tmp/dzlw_Yss_E/concat.3.d.vcf.gz /tmp/dzlw_Yss_E/concat.3.e.vcf.gz /tmp/dzlw_Yss_E/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/dzlw_Yss_E/concat.3.a.bcf /tmp/dzlw_Yss_E/concat.3.b.bcf /tmp/dzlw_Yss_E/concat.3.0.bcf /tmp/dzlw_Yss_E/concat.3.c.bcf /tmp/dzlw_Yss_E/concat.3.d.bcf /tmp/dzlw_Yss_E/concat.3.e.bcf /tmp/dzlw_Yss_E/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/dzlw_Yss_E/concat.3.a.bcf /tmp/dzlw_Yss_E/concat.3.b.bcf /tmp/dzlw_Yss_E/concat.3.0.bcf /tmp/dzlw_Yss_E/concat.3.c.bcf /tmp/dzlw_Yss_E/concat.3.d.bcf /tmp/dzlw_Yss_E/concat.3.e.bcf /tmp/dzlw_Yss_E/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 3511847668 .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/dzlw_Yss_E/naive_concat.0.bcf /tmp/dzlw_Yss_E/naive_concat.1.bcf /tmp/dzlw_Yss_E/naive_concat.2.bcf /tmp/dzlw_Yss_E/naive_concat.3.bcf /tmp/dzlw_Yss_E/naive_concat.4.bcf /tmp/dzlw_Yss_E/naive_concat.5.bcf /tmp/dzlw_Yss_E/naive_concat.6.bcf /tmp/dzlw_Yss_E/naive_concat.7.bcf /tmp/dzlw_Yss_E/naive_concat.8.bcf /tmp/dzlw_Yss_E/naive_concat.9.bcf | /<>/bcftools view -H .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/dzlw_Yss_E/naive_concat.0.vcf.gz /tmp/dzlw_Yss_E/naive_concat.1.vcf.gz /tmp/dzlw_Yss_E/naive_concat.2.vcf.gz /tmp/dzlw_Yss_E/naive_concat.3.vcf.gz /tmp/dzlw_Yss_E/naive_concat.4.vcf.gz /tmp/dzlw_Yss_E/naive_concat.5.vcf.gz /tmp/dzlw_Yss_E/naive_concat.6.vcf.gz /tmp/dzlw_Yss_E/naive_concat.7.vcf.gz /tmp/dzlw_Yss_E/naive_concat.8.vcf.gz /tmp/dzlw_Yss_E/naive_concat.9.vcf.gz | /<>/bcftools view -H .. ok 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/dzlw_Yss_E/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/dzlw_Yss_E/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/dzlw_Yss_E/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/dzlw_Yss_E/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/dzlw_Yss_E/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/dzlw_Yss_E/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/dzlw_Yss_E/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/dzlw_Yss_E/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/dzlw_Yss_E/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/dzlw_Yss_E/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/dzlw_Yss_E/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/dzlw_Yss_E/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/dzlw_Yss_E/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/dzlw_Yss_E/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/dzlw_Yss_E/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/dzlw_Yss_E/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/dzlw_Yss_E/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/dzlw_Yss_E/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/dzlw_Yss_E/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/dzlw_Yss_E/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/dzlw_Yss_E/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/dzlw_Yss_E/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/dzlw_Yss_E/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/dzlw_Yss_E/empty.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/dzlw_Yss_E/rename.map -Ov /tmp/dzlw_Yss_E/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/dzlw_Yss_E/rename.map -Ob /tmp/dzlw_Yss_E/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/dzlw_Yss_E/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/dzlw_Yss_E/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/dzlw_Yss_E/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/convert.vcf.gz | /<>/bcftools convert -g -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/dzlw_Yss_E/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/convert.vcf.gz | /<>/bcftools convert -g .,- 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/dzlw_Yss_E/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/dzlw_Yss_E/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/dzlw_Yss_E/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/dzlw_Yss_E/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/dzlw_Yss_E/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/check.vcf.gz | /<>/bcftools convert -g -,. --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/dzlw_Yss_E/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/check.vcf.gz | /<>/bcftools convert -g .,- --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/dzlw_Yss_E/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/dzlw_Yss_E/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/dzlw_Yss_E/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/convert.vcf.gz | /<>/bcftools convert -h -,.,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/dzlw_Yss_E/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/convert.vcf.gz | /<>/bcftools convert -h .,-,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/dzlw_Yss_E/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/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 ^## .. ok 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 ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples 2>/dev/null | grep -v ^## .. ok 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 ^## .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/dzlw_Yss_E/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/convert.vcf.gz | /<>/bcftools convert --hapsample -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/dzlw_Yss_E/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/convert.vcf.gz | /<>/bcftools convert --hapsample .,- 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools convert --no-version --gvcf2vcf -f /<>/test/gvcf.fa /tmp/dzlw_Yss_E/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/dzlw_Yss_E/convert.gvcf.vcf.gz | /<>/bcftools convert --gvcf2vcf -f /<>/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools .. ok 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/dzlw_Yss_E/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/dzlw_Yss_E/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/dzlw_Yss_E/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/dzlw_Yss_E/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/dzlw_Yss_E/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/dzlw_Yss_E/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/dzlw_Yss_E/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/dzlw_Yss_E/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/dzlw_Yss_E/consensus.vcf.gz -f /<>/test/consensus.fa -i -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/dzlw_Yss_E/consensus.vcf.gz -f /<>/test/consensus.fa -i -m /<>/test/consensus.tab -c /tmp/dzlw_Yss_E/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/dzlw_Yss_E/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/dzlw_Yss_E/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/dzlw_Yss_E/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/dzlw_Yss_E/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/dzlw_Yss_E/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/dzlw_Yss_E/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/dzlw_Yss_E/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/dzlw_Yss_E/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/dzlw_Yss_E/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/dzlw_Yss_E/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/dzlw_Yss_E/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/dzlw_Yss_E/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 .. ok 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 .. 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.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 --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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. 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 -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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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... .. 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/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/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/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... .. 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... .. 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/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/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... .. ok 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/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/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/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/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/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/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/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/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/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/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/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/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 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/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/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/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/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... .. ok 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... .. 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/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/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... .. ok 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... .. ok 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/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... .. ok 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... .. 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-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/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-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-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-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/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/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/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/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/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/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/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/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/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/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... .. 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/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/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 .. 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/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... .. ok 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... .. ok Number of tests: total .. 617 passed .. 561 failed .. 56 Makefile:121: recipe for target 'test' failed make[1]: *** [test] Error 1 make[1]: Leaving directory '/<>' dh_auto_test: make -j4 test returned exit code 2 debian/rules:11: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 20170923-0906 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 20696 Build-Time: 60 Distribution: artful Fail-Stage: build Host Architecture: i386 Install-Time: 11 Job: bcftools_1.4.1-3build1.dsc Machine Architecture: amd64 Package: bcftools Package-Time: 73 Source-Version: 1.4.1-3build1 Space: 20696 Status: attempted Version: 1.4.1-3build1 -------------------------------------------------------------------------------- Finished at 20170923-0906 Build needed 00:01:13, 20696k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13408087 Scanning for processes to kill in build PACKAGEBUILD-13408087 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13408087 Stopping target for build PACKAGEBUILD-13408087 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13408087 Removing build PACKAGEBUILD-13408087