RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux templar 3.13.0-88-generic #135-Ubuntu SMP Wed Jun 8 21:12:41 UTC 2016 aarch64 Buildd toolchain package versions: launchpad-buildd_138 python-lpbuildd_138 sbuild_0.65.2-1ubuntu2~ubuntu14.04.1~ppa8 dpkg-dev_1.17.5ubuntu5.6 python-debian_0.1.27ubuntu1~ubuntu14.04.1~ppa1. Syncing the system clock with the buildd NTP service... 27 Jun 03:47:13 ntpdate[7205]: adjust time server 10.211.37.1 offset -0.128551 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-10059195', '/home/buildd/filecache-default/adaabe0db0cc311cb7f9280668767d876a4b9e43'] Unpacking chroot for build PACKAGEBUILD-10059195 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-10059195'] Mounting chroot for build PACKAGEBUILD-10059195 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-10059195', 'deb http://ftpmaster.internal/ubuntu xenial main universe'] Overriding sources.list in build-PACKAGEBUILD-10059195 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-10059195', 'arm64'] Updating debian chroot for build PACKAGEBUILD-10059195 Hit:1 http://ftpmaster.internal/ubuntu xenial InRelease 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 ['sbuild-package', 'PACKAGEBUILD-10059195', 'arm64', 'xenial', '-c', 'chroot:autobuild', '--arch=arm64', '--dist=xenial', '--purge=never', '--nolog', 'bcftools_1.2-2.dsc'] Initiating build PACKAGEBUILD-10059195 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.13.0-88-generic #135-Ubuntu SMP Wed Jun 8 21:12:41 UTC 2016 aarch64 sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on templar.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ bcftools 1.2-2 (arm64) 27 Jun 2016 03:47 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: bcftools Version: 1.2-2 Source Version: 1.2-2 Distribution: xenial Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/bcftools-SSPauP/bcftools-1.2' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/bcftools-SSPauP' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-10059195/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── bcftools_1.2-2.dsc exists in .; copying to chroot Check architectures ─────────────────── Check dependencies ────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-PleO07/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/«BUILDDIR»/resolver-PleO07/apt_archive ./ InRelease Get:2 copy:/«BUILDDIR»/resolver-PleO07/apt_archive ./ Release [2119 B] Ign:3 copy:/«BUILDDIR»/resolver-PleO07/apt_archive ./ Release.gpg Get:4 copy:/«BUILDDIR»/resolver-PleO07/apt_archive ./ Sources [208 B] Get:5 copy:/«BUILDDIR»/resolver-PleO07/apt_archive ./ Packages [526 B] Fetched 2853 B in 0s (201 kB/s) Reading package lists... W: The repository 'copy:/«BUILDDIR»/resolver-PleO07/apt_archive ./ Release' is not signed. 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 770 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Get:1 copy:/«BUILDDIR»/resolver-PleO07/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 770 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12049 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev, libhts-dev (>= 1.2.1), libgsl-dev, tabix, libio-pty-perl Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev, libhts-dev (>= 1.2.1), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/«BUILDDIR»/resolver-lAbsy9/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. Ign:1 copy:/«BUILDDIR»/resolver-lAbsy9/apt_archive ./ InRelease Get:2 copy:/«BUILDDIR»/resolver-lAbsy9/apt_archive ./ Release [2119 B] Ign:3 copy:/«BUILDDIR»/resolver-lAbsy9/apt_archive ./ Release.gpg Get:4 copy:/«BUILDDIR»/resolver-lAbsy9/apt_archive ./ Sources [452 B] Get:5 copy:/«BUILDDIR»/resolver-lAbsy9/apt_archive ./ Packages [719 B] Fetched 3290 B in 0s (228 kB/s) Reading package lists... W: The repository 'copy:/«BUILDDIR»/resolver-lAbsy9/apt_archive ./ Release' is not signed. 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: autotools-dev bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl2 libhts-dev libhts1 libicu55 libio-pty-perl libmagic1 libpipeline1 libtimedate-perl libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev Suggested packages: wamerican | wordlist whois vacation dh-make gettext-doc autopoint groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs xml-core libmail-sendmail-perl The following NEW packages will be installed: autotools-dev bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl2 libhts-dev libhts1 libicu55 libio-pty-perl libmagic1 libpipeline1 libtimedate-perl libunistring0 libxml2 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 16.2 MB of archives. After this operation, 67.0 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-bcftools-dummy Authentication warning overridden. Get:1 copy:/«BUILDDIR»/resolver-lAbsy9/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [962 B] Get:2 http://ftpmaster.internal/ubuntu xenial/main arm64 groff-base arm64 1.22.3-7 [1122 kB] Get:3 http://ftpmaster.internal/ubuntu xenial/main arm64 bsdmainutils arm64 9.0.6ubuntu3 [170 kB] Get:4 http://ftpmaster.internal/ubuntu xenial/main arm64 libpipeline1 arm64 1.4.1-2 [21.9 kB] Get:5 http://ftpmaster.internal/ubuntu xenial/main arm64 man-db arm64 2.7.5-1 [832 kB] Get:6 http://ftpmaster.internal/ubuntu xenial/main arm64 libunistring0 arm64 0.9.3-5.2ubuntu1 [251 kB] Get:7 http://ftpmaster.internal/ubuntu xenial/main arm64 libmagic1 arm64 1:5.25-2ubuntu1 [209 kB] Get:8 http://ftpmaster.internal/ubuntu xenial/main arm64 file arm64 1:5.25-2ubuntu1 [21.2 kB] Get:9 http://ftpmaster.internal/ubuntu xenial/main arm64 libasprintf0v5 arm64 0.19.7-2ubuntu3 [6420 B] Get:10 http://ftpmaster.internal/ubuntu xenial/main arm64 gettext-base arm64 0.19.7-2ubuntu3 [45.0 kB] Get:11 http://ftpmaster.internal/ubuntu xenial/main arm64 libglib2.0-0 arm64 2.48.0-1ubuntu4 [924 kB] Get:12 http://ftpmaster.internal/ubuntu xenial/main arm64 libicu55 arm64 55.1-7 [7485 kB] Get:13 http://ftpmaster.internal/ubuntu xenial/main arm64 libxml2 arm64 2.9.3+dfsg1-1 [567 kB] Get:14 http://ftpmaster.internal/ubuntu xenial/main arm64 autotools-dev all 20150820.1 [39.8 kB] Get:15 http://ftpmaster.internal/ubuntu xenial/main arm64 libcroco3 arm64 0.6.11-1 [66.0 kB] Get:16 http://ftpmaster.internal/ubuntu xenial/main arm64 gettext arm64 0.19.7-2ubuntu3 [1015 kB] Get:17 http://ftpmaster.internal/ubuntu xenial/main arm64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:18 http://ftpmaster.internal/ubuntu xenial/main arm64 po-debconf all 1.0.19 [234 kB] Get:19 http://ftpmaster.internal/ubuntu xenial/main arm64 libarchive-zip-perl all 1.56-2 [84.1 kB] Get:20 http://ftpmaster.internal/ubuntu xenial/main arm64 libfile-stripnondeterminism-perl all 0.015-1 [10.3 kB] Get:21 http://ftpmaster.internal/ubuntu xenial/main arm64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:22 http://ftpmaster.internal/ubuntu xenial/main arm64 dh-strip-nondeterminism all 0.015-1 [4864 B] Get:23 http://ftpmaster.internal/ubuntu xenial/main arm64 debhelper all 9.20160115ubuntu3 [739 kB] Get:24 http://ftpmaster.internal/ubuntu xenial/main arm64 libgsl2 arm64 2.1+dfsg-2 [691 kB] Get:25 http://ftpmaster.internal/ubuntu xenial/main arm64 libgsl-dev arm64 2.1+dfsg-2 [827 kB] Get:26 http://ftpmaster.internal/ubuntu xenial/universe arm64 libhts1 arm64 1.2.1-2ubuntu1 [189 kB] Get:27 http://ftpmaster.internal/ubuntu xenial/universe arm64 libhts-dev arm64 1.2.1-2ubuntu1 [247 kB] Get:28 http://ftpmaster.internal/ubuntu xenial/main arm64 libio-pty-perl arm64 1:1.08-1.1build1 [29.0 kB] Get:29 http://ftpmaster.internal/ubuntu xenial/universe arm64 tabix arm64 1.2.1-2ubuntu1 [186 kB] Get:30 http://ftpmaster.internal/ubuntu xenial/main arm64 zlib1g-dev arm64 1:1.2.8.dfsg-2ubuntu4 [162 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.2 MB in 25s (631 kB/s) Selecting previously unselected package groff-base. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12049 files and directories currently installed.) Preparing to unpack .../groff-base_1.22.3-7_arm64.deb ... Unpacking groff-base (1.22.3-7) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu3_arm64.deb ... Unpacking bsdmainutils (9.0.6ubuntu3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../libpipeline1_1.4.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.5-1_arm64.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libunistring0:arm64. Preparing to unpack .../libunistring0_0.9.3-5.2ubuntu1_arm64.deb ... Unpacking libunistring0:arm64 (0.9.3-5.2ubuntu1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../libmagic1_1%3a5.25-2ubuntu1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.25-2ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.25-2ubuntu1_arm64.deb ... Unpacking file (1:5.25-2ubuntu1) ... Selecting previously unselected package libasprintf0v5:arm64. Preparing to unpack .../libasprintf0v5_0.19.7-2ubuntu3_arm64.deb ... Unpacking libasprintf0v5:arm64 (0.19.7-2ubuntu3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.7-2ubuntu3_arm64.deb ... Unpacking gettext-base (0.19.7-2ubuntu3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../libglib2.0-0_2.48.0-1ubuntu4_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.48.0-1ubuntu4) ... Selecting previously unselected package libicu55:arm64. Preparing to unpack .../libicu55_55.1-7_arm64.deb ... Unpacking libicu55:arm64 (55.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../libxml2_2.9.3+dfsg1-1_arm64.deb ... Unpacking libxml2:arm64 (2.9.3+dfsg1-1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../autotools-dev_20150820.1_all.deb ... Unpacking autotools-dev (20150820.1) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../libcroco3_0.6.11-1_arm64.deb ... Unpacking libcroco3:arm64 (0.6.11-1) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.19.7-2ubuntu3_arm64.deb ... Unpacking gettext (0.19.7-2ubuntu3) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../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 .../po-debconf_1.0.19_all.deb ... Unpacking po-debconf (1.0.19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../libarchive-zip-perl_1.56-2_all.deb ... Unpacking libarchive-zip-perl (1.56-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../libfile-stripnondeterminism-perl_0.015-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.015-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../dh-strip-nondeterminism_0.015-1_all.deb ... Unpacking dh-strip-nondeterminism (0.015-1) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20160115ubuntu3_all.deb ... Unpacking debhelper (9.20160115ubuntu3) ... Selecting previously unselected package libgsl2:arm64. Preparing to unpack .../libgsl2_2.1+dfsg-2_arm64.deb ... Unpacking libgsl2:arm64 (2.1+dfsg-2) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../libgsl-dev_2.1+dfsg-2_arm64.deb ... Unpacking libgsl-dev (2.1+dfsg-2) ... Selecting previously unselected package libhts1:arm64. Preparing to unpack .../libhts1_1.2.1-2ubuntu1_arm64.deb ... Unpacking libhts1:arm64 (1.2.1-2ubuntu1) ... Selecting previously unselected package libhts-dev:arm64. Preparing to unpack .../libhts-dev_1.2.1-2ubuntu1_arm64.deb ... Unpacking libhts-dev:arm64 (1.2.1-2ubuntu1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1build1_arm64.deb ... Unpacking libio-pty-perl (1:1.08-1.1build1) ... Selecting previously unselected package tabix. Preparing to unpack .../tabix_1.2.1-2ubuntu1_arm64.deb ... Unpacking tabix (1.2.1-2ubuntu1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2ubuntu4_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.8.dfsg-2ubuntu4) ... Selecting previously unselected package sbuild-build-depends-bcftools-dummy. Preparing to unpack .../sbuild-build-depends-bcftools-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up groff-base (1.22.3-7) ... Setting up bsdmainutils (9.0.6ubuntu3) ... 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 libpipeline1:arm64 (1.4.1-2) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libunistring0:arm64 (0.9.3-5.2ubuntu1) ... Setting up libmagic1:arm64 (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up libasprintf0v5:arm64 (0.19.7-2ubuntu3) ... Setting up gettext-base (0.19.7-2ubuntu3) ... Setting up libglib2.0-0:arm64 (2.48.0-1ubuntu4) ... No schema files found: doing nothing. Setting up libicu55:arm64 (55.1-7) ... Setting up libxml2:arm64 (2.9.3+dfsg1-1) ... Setting up autotools-dev (20150820.1) ... Setting up libcroco3:arm64 (0.6.11-1) ... Setting up gettext (0.19.7-2ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.19) ... Setting up libarchive-zip-perl (1.56-2) ... Setting up libfile-stripnondeterminism-perl (0.015-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libgsl2:arm64 (2.1+dfsg-2) ... Setting up libgsl-dev (2.1+dfsg-2) ... Setting up libhts1:arm64 (1.2.1-2ubuntu1) ... Setting up libhts-dev:arm64 (1.2.1-2ubuntu1) ... Setting up libio-pty-perl (1:1.08-1.1build1) ... Setting up tabix (1.2.1-2ubuntu1) ... Setting up zlib1g-dev:arm64 (1:1.2.8.dfsg-2ubuntu4) ... Setting up debhelper (9.20160115ubuntu3) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.015-1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.13.0-88-generic arm64 (aarch64) Toolchain package versions: binutils_2.26-8ubuntu2 dpkg-dev_1.18.4ubuntu1 g++-5_5.3.1-14ubuntu2 gcc-5_5.3.1-14ubuntu2 libc6-dev_2.23-0ubuntu3 libstdc++-5-dev_5.3.1-14ubuntu2 libstdc++6_5.3.1-14ubuntu2 linux-libc-dev_4.4.0-21.37 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.2.10ubuntu1 apt-transport-https_1.2.10ubuntu1 autotools-dev_20150820.1 base-files_9.4ubuntu4 base-passwd_3.5.39 bash_4.3-14ubuntu1 binutils_2.26-8ubuntu2 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.27.1-6ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20160104ubuntu1 coreutils_8.25-2ubuntu2 cpp_4:5.3.1-1ubuntu1 cpp-5_5.3.1-14ubuntu2 dash_0.5.8-2.1ubuntu2 debconf_1.5.58ubuntu1 debhelper_9.20160115ubuntu3 debianutils_4.7 dh-strip-nondeterminism_0.015-1 diffutils_1:3.3-3 dmsetup_2:1.02.110-1ubuntu10 dpkg_1.18.4ubuntu1 dpkg-dev_1.18.4ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1ubuntu1 g++-5_5.3.1-14ubuntu2 gcc_4:5.3.1-1ubuntu1 gcc-5_5.3.1-14ubuntu2 gcc-5-base_5.3.1-14ubuntu2 gcc-6-base_6.0.1-0ubuntu1 gettext_0.19.7-2ubuntu3 gettext-base_0.19.7-2ubuntu3 gnupg_1.4.20-1ubuntu3 gpgv_1.4.20-1ubuntu3 grep_2.24-1 groff-base_1.22.3-7 gzip_1.6-4ubuntu1 hostname_3.16ubuntu2 init_1.29ubuntu1 init-system-helpers_1.29ubuntu1 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-0ubuntu2 libapt-pkg5.0_1.2.10ubuntu1 libarchive-zip-perl_1.56-2 libasan2_5.3.1-14ubuntu2 libasn1-8-heimdal_1.7~git20150920+dfsg-4ubuntu1 libasprintf0v5_0.19.7-2ubuntu3 libatomic1_5.3.1-14ubuntu2 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1ubuntu2 libaudit1_1:2.4.5-1ubuntu2 libblkid1_2.27.1-6ubuntu3 libbz2-1.0_1.0.6-8 libc-bin_2.23-0ubuntu3 libc-dev-bin_2.23-0ubuntu3 libc6_2.23-0ubuntu3 libc6-dev_2.23-0ubuntu3 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-14ubuntu2 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcurl3-gnutls_7.47.0-1ubuntu2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1ubuntu3 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.110-1ubuntu10 libdpkg-perl_1.18.4ubuntu1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-6ubuntu3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.015-1 libgcc-5-dev_5.3.1-14ubuntu2 libgcc1_1:6.0.1-0ubuntu1 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.48.0-1ubuntu4 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.10-4ubuntu1 libgomp1_5.3.1-14ubuntu2 libgpg-error0_1.21-2ubuntu1 libgsl-dev_2.1+dfsg-2 libgsl2_2.1+dfsg-2 libgssapi-krb5-2_1.13.2+dfsg-5 libgssapi3-heimdal_1.7~git20150920+dfsg-4ubuntu1 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libpam-modules-bin_1.1.8-3.2ubuntu2 libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpcre3_2:8.38-3.1 libperl5.22_5.22.1-9 libpipeline1_1.4.1-2 libpng12-0_1.2.54-1ubuntu1 libprocps4_2:3.3.10-4ubuntu2 libreadline6_6.3-8ubuntu2 libroken18-heimdal_1.7~git20150920+dfsg-4ubuntu1 librtmp1_2.4+20151223.gitfa8646d-1build1 libsasl2-2_2.1.26.dfsg1-14build1 libsasl2-modules-db_2.1.26.dfsg1-14build1 libseccomp2_2.2.3-3ubuntu3 libselinux1_2.4-3build2 libsemanage-common_2.3-1build3 libsemanage1_2.3-1build3 libsepol1_2.4-2 libslang2_2.3.0-2ubuntu1 libsmartcols1_2.27.1-6ubuntu3 libsqlite3-0_3.11.0-1ubuntu1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2g-1ubuntu4 libstdc++-5-dev_5.3.1-14ubuntu2 libstdc++6_5.3.1-14ubuntu2 libsystemd0_229-4ubuntu4 libtasn1-6_4.7-3 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1ubuntu1 libubsan0_5.3.1-14ubuntu2 libudev1_229-4ubuntu4 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6ubuntu3 libwind0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libxml2_2.9.3+dfsg1-1 linux-libc-dev_4.4.0-21.37 lockfile-progs_0.1.17 login_1:4.2-3.1ubuntu5 lsb-base_9.20160110 make_4.1-6 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.27.1-6ubuntu3 multiarch-support_2.23-0ubuntu3 ncurses-base_6.0+20160213-1ubuntu1 ncurses-bin_6.0+20160213-1ubuntu1 openssl_1.0.2g-1ubuntu4 optipng_0.7.6-1 passwd_1:4.2-3.1ubuntu5 patch_2.7.5-1 perl_5.22.1-9 perl-base_5.22.1-9 perl-modules-5.22_5.22.1-9 pkg-create-dbgsym_0.72 pkgbinarymangler_129 po-debconf_1.0.19 policyrcd-script-zg2_0.1-2 procps_2:3.3.10-4ubuntu2 readline-common_6.3-8ubuntu2 sbuild-build-depends-bcftools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-7 sensible-utils_0.0.9 systemd_229-4ubuntu4 systemd-sysv_229-4ubuntu4 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.3ubuntu2 tabix_1.2.1-2ubuntu1 tar_1.28-2.1 tzdata_2016d-0ubuntu0.16.04 ubuntu-keyring_2012.05.19 util-linux_2.27.1-6ubuntu3 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4 zlib1g-dev_1:1.2.8.dfsg-2ubuntu4 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Sat Jan 23 02:54:32 2016 UTC using RSA key ID AFE826FB gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./bcftools_1.2-2.dsc dpkg-source: info: extracting bcftools in bcftools-1.2 dpkg-source: info: unpacking bcftools_1.2.orig.tar.gz dpkg-source: info: unpacking bcftools_1.2-2.debian.tar.xz dpkg-source: info: applying improve-plugin-support.patch 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 spelling.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=8 HOME=/home/buildd LANG=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/«PKGBUILDDIR» SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: source package bcftools dpkg-buildpackage: source version 1.2-2 dpkg-buildpackage: source distribution unstable dpkg-source --before-build bcftools-1.2 dpkg-buildpackage: host architecture arm64 fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel make -j8 distclean make[1]: Entering directory '/«PKGBUILDDIR»' rm -f test/*.o test/*~ test/test-rbuf rm -f plugins/*.so plugins/*.P 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 '/«PKGBUILDDIR»' dh_clean -O--parallel debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel dh_update_autotools_config -a -O--parallel dh_auto_configure -a -O--parallel dh_auto_build -a -O--parallel make -j8 make[1]: Entering directory '/«PKGBUILDDIR»' echo '#define BCFTOOLS_VERSION "1.2"' > version.h cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfindex.c -o vcfindex.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include tabix.c -o tabix.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfstats.c -o vcfstats.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfisec.c -o vcfisec.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfmerge.c -o vcfmerge.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfquery.c -o vcfquery.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcffilter.c -o vcffilter.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include filter.c -o filter.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfsom.c -o vcfsom.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfnorm.c -o vcfnorm.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfgtcheck.c -o vcfgtcheck.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfview.c -o vcfview.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfannotate.c -o vcfannotate.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfroh.c -o vcfroh.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfconcat.c -o vcfconcat.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfcall.c -o vcfcall.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include mcall.c -o mcall.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcmp.c -o vcmp.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include gvcf.c -o gvcf.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include reheader.c -o reheader.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include convert.c -o convert.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfconvert.c -o vcfconvert.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include tsv2vcf.c -o tsv2vcf.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfcnv.c -o vcfcnv.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include HMM.c -o HMM.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfplugin.c -o vcfplugin.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include consensus.c -o consensus.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include ploidy.c -o ploidy.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include version.c -o version.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include ccall.c -o ccall.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include em.c -o em.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include prob1.c -o prob1.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include kmin.c -o kmin.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include polysomy.c -o polysomy.o cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include test/test-rbuf.c -o test/test-rbuf.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include -fPIC -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include -fPIC -shared -o plugins/fixploidy.so ploidy.c version.c plugins/fixploidy.c -lhts -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include -fPIC -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include -fPIC -shared -o plugins/vcf2sex.so ploidy.c version.c plugins/vcf2sex.c -lhts -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include -fPIC -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include -fPIC -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include -fPIC -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include -fPIC -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include main.c -o main.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -o test/test-rbuf -lm -ldl test/test-rbuf.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/aarch64-linux-gnu/bcftools\" -DUSE_GPL -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 version.o ccall.o em.o prob1.o kmin.o polysomy.o -lpthread -lz -lm -ldl -lhts -lgsl -lgslcblas -Wl,-Bsymbolic-functions -Wl,-z,relro make[1]: Leaving directory '/«PKGBUILDDIR»' dh_auto_test -a -O--parallel make -j8 test make[1]: Entering directory '/«PKGBUILDDIR»' ./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 filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: /usr/bin/tabix /tmp/Qyl6m9GNFO/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /«PKGBUILDDIR»/bcftools view -H /tmp/Qyl6m9GNFO/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: /usr/bin/tabix /tmp/Qyl6m9GNFO/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /«PKGBUILDDIR»/bcftools view -H /tmp/Qyl6m9GNFO/merge.a.bcf 1:3000151-3000151 .. ok test_tabix: /usr/bin/tabix /tmp/Qyl6m9GNFO/large_chrom_tbi_limit.vcf.gz chr11:1-536870912 .. ok test_tabix: /«PKGBUILDDIR»/bcftools view -H /tmp/Qyl6m9GNFO/large_chrom_tbi_limit.bcf chr11:1-536870912 .. ok test_index: /«PKGBUILDDIR»/bcftools view -H /tmp/Qyl6m9GNFO/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /«PKGBUILDDIR»/bcftools view -H /tmp/Qyl6m9GNFO/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /«PKGBUILDDIR»/bcftools view -H /tmp/Qyl6m9GNFO/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /«PKGBUILDDIR»/bcftools view -H /tmp/Qyl6m9GNFO/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /«PKGBUILDDIR»/bcftools index -s /tmp/Qyl6m9GNFO/idx.vcf.gz .. ok test_vcf_idxstats: /«PKGBUILDDIR»/bcftools index -s /tmp/Qyl6m9GNFO/idx.vcf.gz .. ok test_vcf_idxstats: /«PKGBUILDDIR»/bcftools index -s /tmp/Qyl6m9GNFO/idx.bcf .. ok test_vcf_idxstats: /«PKGBUILDDIR»/bcftools index -n /tmp/Qyl6m9GNFO/idx.vcf.gz .. ok test_vcf_idxstats: /«PKGBUILDDIR»/bcftools index -n /tmp/Qyl6m9GNFO/idx.vcf.gz .. ok test_vcf_idxstats: /«PKGBUILDDIR»/bcftools index -n /tmp/Qyl6m9GNFO/idx.bcf .. ok test_vcf_idxstats: /«PKGBUILDDIR»/bcftools index -s /tmp/Qyl6m9GNFO/empty.vcf.gz .. ok test_vcf_idxstats: /«PKGBUILDDIR»/bcftools index -s /tmp/Qyl6m9GNFO/empty.vcf.gz .. ok test_vcf_idxstats: /«PKGBUILDDIR»/bcftools index -s /tmp/Qyl6m9GNFO/empty.bcf .. ok test_vcf_idxstats: /«PKGBUILDDIR»/bcftools index -n /tmp/Qyl6m9GNFO/empty.vcf.gz Warning: The index file is older than the data file: /tmp/Qyl6m9GNFO/empty.vcf.gz.csi Warning: The index file is older than the data file: /tmp/Qyl6m9GNFO/empty.vcf.gz.csi .. ok test_vcf_idxstats: /«PKGBUILDDIR»/bcftools index -n /tmp/Qyl6m9GNFO/empty.vcf.gz .. ok test_vcf_idxstats: /«PKGBUILDDIR»/bcftools index -n /tmp/Qyl6m9GNFO/empty.bcf .. ok test_vcf_check: /«PKGBUILDDIR»/bcftools stats -s - /tmp/Qyl6m9GNFO/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/check.vcf.gz | /«PKGBUILDDIR»/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /«PKGBUILDDIR»/bcftools stats -s - /tmp/Qyl6m9GNFO/stats.a.vcf.gz /tmp/Qyl6m9GNFO/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /«PKGBUILDDIR»/bcftools isec -n =2 /tmp/Qyl6m9GNFO/isec.a.vcf.gz /tmp/Qyl6m9GNFO/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /«PKGBUILDDIR»/bcftools isec -Ob -n =2 /tmp/Qyl6m9GNFO/isec.a.vcf.gz /tmp/Qyl6m9GNFO/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /«PKGBUILDDIR»/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/Qyl6m9GNFO/isec.a.vcf.gz /tmp/Qyl6m9GNFO/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /«PKGBUILDDIR»/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/Qyl6m9GNFO/isec.a.vcf.gz /tmp/Qyl6m9GNFO/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /«PKGBUILDDIR»/bcftools isec -n =2 -c both /tmp/Qyl6m9GNFO/isec.a.vcf.gz /tmp/Qyl6m9GNFO/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /«PKGBUILDDIR»/bcftools isec -Ob -n =2 -c both /tmp/Qyl6m9GNFO/isec.a.vcf.gz /tmp/Qyl6m9GNFO/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /«PKGBUILDDIR»/bcftools isec -n =2 -c any /tmp/Qyl6m9GNFO/isec.a.vcf.gz /tmp/Qyl6m9GNFO/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /«PKGBUILDDIR»/bcftools isec -Ob -n =2 -c any /tmp/Qyl6m9GNFO/isec.a.vcf.gz /tmp/Qyl6m9GNFO/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /«PKGBUILDDIR»/bcftools isec -C -c any /tmp/Qyl6m9GNFO/isec.a.vcf.gz /tmp/Qyl6m9GNFO/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /«PKGBUILDDIR»/bcftools isec -Ob -C -c any /tmp/Qyl6m9GNFO/isec.a.vcf.gz /tmp/Qyl6m9GNFO/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec2: /«PKGBUILDDIR»/bcftools isec -T /tmp/Qyl6m9GNFO/isec.tab.gz /tmp/Qyl6m9GNFO/isec.a.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_isec2: /«PKGBUILDDIR»/bcftools isec -Ob -T /tmp/Qyl6m9GNFO/isec.tab.gz /tmp/Qyl6m9GNFO/isec.a.vcf.gz 2>/dev/null | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /«PKGBUILDDIR»/bcftools merge --force-samples /tmp/Qyl6m9GNFO/merge.a.vcf.gz /tmp/Qyl6m9GNFO/merge.b.vcf.gz /tmp/Qyl6m9GNFO/merge.c.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_merge: /«PKGBUILDDIR»/bcftools merge -Ob --force-samples /tmp/Qyl6m9GNFO/merge.a.vcf.gz /tmp/Qyl6m9GNFO/merge.b.vcf.gz /tmp/Qyl6m9GNFO/merge.c.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /«PKGBUILDDIR»/bcftools merge --force-samples -m none /tmp/Qyl6m9GNFO/merge.2.a.vcf.gz /tmp/Qyl6m9GNFO/merge.2.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_merge: /«PKGBUILDDIR»/bcftools merge -Ob --force-samples -m none /tmp/Qyl6m9GNFO/merge.2.a.vcf.gz /tmp/Qyl6m9GNFO/merge.2.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /«PKGBUILDDIR»/bcftools merge --force-samples -m both /tmp/Qyl6m9GNFO/merge.2.a.vcf.gz /tmp/Qyl6m9GNFO/merge.2.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_merge: /«PKGBUILDDIR»/bcftools merge -Ob --force-samples -m both /tmp/Qyl6m9GNFO/merge.2.a.vcf.gz /tmp/Qyl6m9GNFO/merge.2.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /«PKGBUILDDIR»/bcftools merge --force-samples -m all /tmp/Qyl6m9GNFO/merge.2.a.vcf.gz /tmp/Qyl6m9GNFO/merge.2.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_merge: /«PKGBUILDDIR»/bcftools merge -Ob --force-samples -m all /tmp/Qyl6m9GNFO/merge.2.a.vcf.gz /tmp/Qyl6m9GNFO/merge.2.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /«PKGBUILDDIR»/bcftools merge --force-samples -i TR:sum,TA:sum,TG:sum /tmp/Qyl6m9GNFO/merge.3.a.vcf.gz /tmp/Qyl6m9GNFO/merge.3.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_merge: /«PKGBUILDDIR»/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/Qyl6m9GNFO/merge.3.a.vcf.gz /tmp/Qyl6m9GNFO/merge.3.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /«PKGBUILDDIR»/bcftools merge --force-samples -m id /tmp/Qyl6m9GNFO/merge.4.a.vcf.gz /tmp/Qyl6m9GNFO/merge.4.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_merge: /«PKGBUILDDIR»/bcftools merge -Ob --force-samples -m id /tmp/Qyl6m9GNFO/merge.4.a.vcf.gz /tmp/Qyl6m9GNFO/merge.4.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/Qyl6m9GNFO/query.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/Qyl6m9GNFO/view.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/Qyl6m9GNFO/view.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/Qyl6m9GNFO/view.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/Qyl6m9GNFO/view.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/Qyl6m9GNFO/view.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' /tmp/Qyl6m9GNFO/view.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/Qyl6m9GNFO/view.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' /tmp/Qyl6m9GNFO/view.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' /tmp/Qyl6m9GNFO/query.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/Qyl6m9GNFO/query.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/Qyl6m9GNFO/query.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' /tmp/Qyl6m9GNFO/query.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/Qyl6m9GNFO/view.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/view.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/Qyl6m9GNFO/query.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/Qyl6m9GNFO/query.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/Qyl6m9GNFO/query.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/Qyl6m9GNFO/query.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /«PKGBUILDDIR»/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/Qyl6m9GNFO/view.vectors.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/view.vectors.vcf.gz | /«PKGBUILDDIR»/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: /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' /tmp/Qyl6m9GNFO/query.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' /tmp/Qyl6m9GNFO/query.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' /tmp/Qyl6m9GNFO/query.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' /tmp/Qyl6m9GNFO/query.filter.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.filter.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/Qyl6m9GNFO/query.2.vcf.gz .. ok test_vcf_query: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/query.2.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_norm: /«PKGBUILDDIR»/bcftools norm -f /«PKGBUILDDIR»/test/norm.fa /tmp/Qyl6m9GNFO/norm.vcf.gz | grep -v ^##bcftools_ Lines total/modified/skipped: 21/13/0 .. ok test_vcf_norm: /«PKGBUILDDIR»/bcftools norm -Ob -f /«PKGBUILDDIR»/test/norm.fa /tmp/Qyl6m9GNFO/norm.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ Lines total/modified/skipped: 21/13/0 .. ok test_vcf_norm: /«PKGBUILDDIR»/bcftools norm -m- /tmp/Qyl6m9GNFO/norm.split.vcf.gz | grep -v ^##bcftools_ Lines total/modified/skipped: 18/0/0 .. ok test_vcf_norm: /«PKGBUILDDIR»/bcftools norm -Ob -m- /tmp/Qyl6m9GNFO/norm.split.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ Lines total/modified/skipped: 18/0/0 .. ok test_vcf_norm: /«PKGBUILDDIR»/bcftools norm -m+ /tmp/Qyl6m9GNFO/norm.merge.vcf.gz | grep -v ^##bcftools_ Lines total/modified/skipped: 26/0/0 .. ok test_vcf_norm: /«PKGBUILDDIR»/bcftools norm -Ob -m+ /tmp/Qyl6m9GNFO/norm.merge.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ Lines total/modified/skipped: 26/0/0 .. ok test_vcf_norm: /«PKGBUILDDIR»/bcftools norm -m+ -s /tmp/Qyl6m9GNFO/norm.merge.vcf.gz | grep -v ^##bcftools_ Lines total/modified/skipped: 26/0/0 .. ok test_vcf_norm: /«PKGBUILDDIR»/bcftools norm -Ob -m+ -s /tmp/Qyl6m9GNFO/norm.merge.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ Lines total/modified/skipped: 26/0/0 .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -aUc1 -C1 -s NA00002 -v snps /tmp/Qyl6m9GNFO/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/Qyl6m9GNFO/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -f PASS -Xks NA00003 /tmp/Qyl6m9GNFO/view.vcf.gz -r20,Y | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -f PASS -Xks NA00003 /tmp/Qyl6m9GNFO/view.vcf.gz -r20,Y | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -xs NA00003 /tmp/Qyl6m9GNFO/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -xs NA00003 /tmp/Qyl6m9GNFO/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/Qyl6m9GNFO/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/Qyl6m9GNFO/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -p /tmp/Qyl6m9GNFO/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -p /tmp/Qyl6m9GNFO/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -P /tmp/Qyl6m9GNFO/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -P /tmp/Qyl6m9GNFO/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -hm2 -M2 -q0.3 -Q0.7 /tmp/Qyl6m9GNFO/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/Qyl6m9GNFO/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Hu /tmp/Qyl6m9GNFO/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -GVsnps /tmp/Qyl6m9GNFO/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -GVsnps /tmp/Qyl6m9GNFO/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -ne 'INDEL=1 || PV4[0]<0.006' /tmp/Qyl6m9GNFO/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/Qyl6m9GNFO/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -s ^NA00003 /tmp/Qyl6m9GNFO/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -s ^NA00003 /tmp/Qyl6m9GNFO/view.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view /tmp/Qyl6m9GNFO/view.omitgenotypes.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/view.omitgenotypes.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -asA /tmp/Qyl6m9GNFO/view.vectors.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -asA /tmp/Qyl6m9GNFO/view.vectors.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -asB /tmp/Qyl6m9GNFO/view.vectors.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -asB /tmp/Qyl6m9GNFO/view.vectors.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -H -i'FMT/FGS[0]="AAAAAA"' /tmp/Qyl6m9GNFO/view.filter.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -H -i'FMT/FGS[2]="C"' /tmp/Qyl6m9GNFO/view.filter.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -H -i'FMT/FGS[4]="EE"' /tmp/Qyl6m9GNFO/view.filter.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -H -i'FMT/FRS[1]="BB"' /tmp/Qyl6m9GNFO/view.filter.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -H -i'TXT0="text"' /tmp/Qyl6m9GNFO/view.filter.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -T /«PKGBUILDDIR»/test/view.chrs.tab /tmp/Qyl6m9GNFO/view.chrs.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -Ob -T /«PKGBUILDDIR»/test/view.chrs.tab /tmp/Qyl6m9GNFO/view.chrs.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -S. -e'TXT0="text"' /«PKGBUILDDIR»/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -S. -e'TXT0="text"' /«PKGBUILDDIR»/test/view.filter.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -S. -e'FMT/FRS[1]="BB"' /«PKGBUILDDIR»/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -S. -e'FMT/FRS[1]="BB"' /«PKGBUILDDIR»/test/view.filter.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -S. -e'FMT/FGS[0]="AAAAAA"' /«PKGBUILDDIR»/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -S. -e'FMT/FGS[0]="AAAAAA"' /«PKGBUILDDIR»/test/view.filter.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -S. -e'FMT/FGS[1]="BBB"' /«PKGBUILDDIR»/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -S. -e'FMT/FGS[1]="BBB"' /«PKGBUILDDIR»/test/view.filter.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -S. -e'FMT/FGS[4]="EE"' /«PKGBUILDDIR»/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -S. -e'FMT/FGS[4]="EE"' /«PKGBUILDDIR»/test/view.filter.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -S. -e'FMT/STR="XX"' /«PKGBUILDDIR»/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -S. -e'FMT/STR="XX"' /«PKGBUILDDIR»/test/view.filter.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -H -C5:nonmajor /tmp/Qyl6m9GNFO/view.minmaxac.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -H -c6:nonmajor /tmp/Qyl6m9GNFO/view.minmaxac.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /«PKGBUILDDIR»/bcftools view -H -q0.3:major /tmp/Qyl6m9GNFO/view.minmaxac.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_call: /«PKGBUILDDIR»/bcftools call -mv /«PKGBUILDDIR»/test/mpileup.vcf | grep -v ^##bcftools_ .. ok test_vcf_call: /«PKGBUILDDIR»/bcftools call -Ob -mv /«PKGBUILDDIR»/test/mpileup.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /«PKGBUILDDIR»/bcftools call -mvg0 /«PKGBUILDDIR»/test/mpileup.vcf | grep -v ^##bcftools_ .. ok test_vcf_call: /«PKGBUILDDIR»/bcftools call -Ob -mvg0 /«PKGBUILDDIR»/test/mpileup.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /«PKGBUILDDIR»/bcftools call -mA -C alleles -T /tmp/Qyl6m9GNFO/mpileup.tab.gz /«PKGBUILDDIR»/test/mpileup.vcf | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /«PKGBUILDDIR»/bcftools call -Ob -mA -C alleles -T /tmp/Qyl6m9GNFO/mpileup.tab.gz /«PKGBUILDDIR»/test/mpileup.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -mx -g2 -G2 /«PKGBUILDDIR»/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -mx -g2 -G2 /«PKGBUILDDIR»/test/filter.1.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /«PKGBUILDDIR»/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -e'DP=19' /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -e'DP=19' /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -e'DP=19' -s XX /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -e'DP=19' -s XX /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -e'DP=19' -s XX -m+ /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -e'DP=19' -s XX -m+ /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -e'DP=19' -s XX -mx /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -e'DP=19' -s XX -mx /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -e'DP=19' -s XX -m+x /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -e'DP=19' -s XX -m+x /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -e'FMT/GT="0/2"' /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -e'FMT/GT="0/2"' /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -e'FMT/GT="0/2"' -s XX /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /«PKGBUILDDIR»/test/filter.3.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /«PKGBUILDDIR»/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /«PKGBUILDDIR»/test/filter.2.vcf | /«PKGBUILDDIR»/bcftools view | /«PKGBUILDDIR»/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_regions: /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /«PKGBUILDDIR»/test/regions.tab /tmp/Qyl6m9GNFO/regions.vcf.gz .. ok test_vcf_regions: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/regions.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /«PKGBUILDDIR»/test/regions.tab .. ok test_vcf_regions: /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /«PKGBUILDDIR»/test/regions.tab /tmp/Qyl6m9GNFO/regions.vcf.gz .. ok test_vcf_regions: /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Qyl6m9GNFO/regions.tab.gz /tmp/Qyl6m9GNFO/regions.vcf.gz .. ok test_vcf_regions: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/regions.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Qyl6m9GNFO/regions.tab.gz .. ok test_vcf_regions: /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/Qyl6m9GNFO/regions.tab.gz /tmp/Qyl6m9GNFO/regions.vcf.gz .. ok test_vcf_regions: /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Qyl6m9GNFO/regions.bed /tmp/Qyl6m9GNFO/regions.vcf.gz .. ok test_vcf_regions: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/regions.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Qyl6m9GNFO/regions.bed .. ok test_vcf_regions: /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/Qyl6m9GNFO/regions.bed /tmp/Qyl6m9GNFO/regions.vcf.gz .. ok test_vcf_regions: /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Qyl6m9GNFO/regions.bed.gz /tmp/Qyl6m9GNFO/regions.vcf.gz .. ok test_vcf_regions: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/regions.vcf.gz | /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Qyl6m9GNFO/regions.bed.gz .. ok test_vcf_regions: /«PKGBUILDDIR»/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/Qyl6m9GNFO/regions.bed.gz /tmp/Qyl6m9GNFO/regions.vcf.gz .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -a /tmp/Qyl6m9GNFO/annotate.tab.gz -h /«PKGBUILDDIR»/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /«PKGBUILDDIR»/test/annotate.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/Qyl6m9GNFO/annotate.tab.gz -h /«PKGBUILDDIR»/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /«PKGBUILDDIR»/test/annotate.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -a /tmp/Qyl6m9GNFO/annotate2.tab.gz -h /«PKGBUILDDIR»/test/annotate.hdr -c CHROM,FROM,TO,T_STR /«PKGBUILDDIR»/test/annotate.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/Qyl6m9GNFO/annotate2.tab.gz -h /«PKGBUILDDIR»/test/annotate.hdr -c CHROM,FROM,TO,T_STR /«PKGBUILDDIR»/test/annotate.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -a /tmp/Qyl6m9GNFO/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/Qyl6m9GNFO/annotate.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/Qyl6m9GNFO/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/Qyl6m9GNFO/annotate.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -a /tmp/Qyl6m9GNFO/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/Qyl6m9GNFO/annotate2.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ 2 sample(s) in common .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/Qyl6m9GNFO/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/Qyl6m9GNFO/annotate2.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ 2 sample(s) in common .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -a /tmp/Qyl6m9GNFO/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/Qyl6m9GNFO/annotate2.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/Qyl6m9GNFO/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/Qyl6m9GNFO/annotate2.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /«PKGBUILDDIR»/test/annotate3.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /«PKGBUILDDIR»/test/annotate3.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -x FORMAT /«PKGBUILDDIR»/test/annotate3.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -Ob -x FORMAT /«PKGBUILDDIR»/test/annotate3.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -a /tmp/Qyl6m9GNFO/annots4.vcf.gz -c +INFO /tmp/Qyl6m9GNFO/annotate4.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/Qyl6m9GNFO/annots4.vcf.gz -c +INFO /tmp/Qyl6m9GNFO/annotate4.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -a /tmp/Qyl6m9GNFO/annots4.tab.gz -h /«PKGBUILDDIR»/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /«PKGBUILDDIR»/test/annotate4.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /«PKGBUILDDIR»/bcftools annotate -Ob -a /tmp/Qyl6m9GNFO/annots4.tab.gz -h /«PKGBUILDDIR»/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /«PKGBUILDDIR»/test/annotate4.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat /tmp/Qyl6m9GNFO/concat.1.a.vcf.gz /tmp/Qyl6m9GNFO/concat.1.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -Ob /tmp/Qyl6m9GNFO/concat.1.a.vcf.gz /tmp/Qyl6m9GNFO/concat.1.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat /tmp/Qyl6m9GNFO/concat.1.a.bcf /tmp/Qyl6m9GNFO/concat.1.b.bcf | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -Ob /tmp/Qyl6m9GNFO/concat.1.a.bcf /tmp/Qyl6m9GNFO/concat.1.b.bcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -a /tmp/Qyl6m9GNFO/concat.2.a.vcf.gz /tmp/Qyl6m9GNFO/concat.2.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -Ob -a /tmp/Qyl6m9GNFO/concat.2.a.vcf.gz /tmp/Qyl6m9GNFO/concat.2.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -a /tmp/Qyl6m9GNFO/concat.2.a.bcf /tmp/Qyl6m9GNFO/concat.2.b.bcf | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -Ob -a /tmp/Qyl6m9GNFO/concat.2.a.bcf /tmp/Qyl6m9GNFO/concat.2.b.bcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -aD /tmp/Qyl6m9GNFO/concat.2.a.vcf.gz /tmp/Qyl6m9GNFO/concat.2.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -Ob -aD /tmp/Qyl6m9GNFO/concat.2.a.vcf.gz /tmp/Qyl6m9GNFO/concat.2.b.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -aD /tmp/Qyl6m9GNFO/concat.2.a.bcf /tmp/Qyl6m9GNFO/concat.2.b.bcf | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -Ob -aD /tmp/Qyl6m9GNFO/concat.2.a.bcf /tmp/Qyl6m9GNFO/concat.2.b.bcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -l /tmp/Qyl6m9GNFO/concat.3.a.vcf.gz /tmp/Qyl6m9GNFO/concat.3.b.vcf.gz /tmp/Qyl6m9GNFO/concat.3.0.vcf.gz /tmp/Qyl6m9GNFO/concat.3.c.vcf.gz /tmp/Qyl6m9GNFO/concat.3.d.vcf.gz /tmp/Qyl6m9GNFO/concat.3.e.vcf.gz /tmp/Qyl6m9GNFO/concat.3.f.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -Ob -l /tmp/Qyl6m9GNFO/concat.3.a.vcf.gz /tmp/Qyl6m9GNFO/concat.3.b.vcf.gz /tmp/Qyl6m9GNFO/concat.3.0.vcf.gz /tmp/Qyl6m9GNFO/concat.3.c.vcf.gz /tmp/Qyl6m9GNFO/concat.3.d.vcf.gz /tmp/Qyl6m9GNFO/concat.3.e.vcf.gz /tmp/Qyl6m9GNFO/concat.3.f.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -l /tmp/Qyl6m9GNFO/concat.3.a.bcf /tmp/Qyl6m9GNFO/concat.3.b.bcf /tmp/Qyl6m9GNFO/concat.3.0.bcf /tmp/Qyl6m9GNFO/concat.3.c.bcf /tmp/Qyl6m9GNFO/concat.3.d.bcf /tmp/Qyl6m9GNFO/concat.3.e.bcf /tmp/Qyl6m9GNFO/concat.3.f.bcf | grep -v ^##bcftools_ .. ok test_vcf_concat: /«PKGBUILDDIR»/bcftools concat -Ob -l /tmp/Qyl6m9GNFO/concat.3.a.bcf /tmp/Qyl6m9GNFO/concat.3.b.bcf /tmp/Qyl6m9GNFO/concat.3.0.bcf /tmp/Qyl6m9GNFO/concat.3.c.bcf /tmp/Qyl6m9GNFO/concat.3.d.bcf /tmp/Qyl6m9GNFO/concat.3.e.bcf /tmp/Qyl6m9GNFO/concat.3.f.bcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.hdr /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.hdr | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.hdr /tmp/Qyl6m9GNFO/reheader.bcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /tmp/Qyl6m9GNFO/reheader.bcf | /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.hdr | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.hdr /tmp/Qyl6m9GNFO/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /tmp/Qyl6m9GNFO/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools reheader -h /«PKGBUILDDIR»/test/reheader.hdr | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples /tmp/Qyl6m9GNFO/reheader.bcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /tmp/Qyl6m9GNFO/reheader.bcf | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples /tmp/Qyl6m9GNFO/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /tmp/Qyl6m9GNFO/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples2 /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /«PKGBUILDDIR»/test/reheader.vcf | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples2 | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples2 /tmp/Qyl6m9GNFO/reheader.bcf | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /tmp/Qyl6m9GNFO/reheader.bcf | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples2 | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples2 /tmp/Qyl6m9GNFO/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /tmp/Qyl6m9GNFO/reheader.vcf.gz | /«PKGBUILDDIR»/bcftools reheader -s /«PKGBUILDDIR»/test/reheader.samples2 | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ .. ok test_rename_chrs: /«PKGBUILDDIR»/bcftools annotate --rename-chrs /tmp/Qyl6m9GNFO/rename.map -Ov /tmp/Qyl6m9GNFO/annotate.bcf | /«PKGBUILDDIR»/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /«PKGBUILDDIR»/bcftools annotate --rename-chrs /tmp/Qyl6m9GNFO/rename.map -Ob /tmp/Qyl6m9GNFO/annotate.bcf | /«PKGBUILDDIR»/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /«PKGBUILDDIR»/bcftools annotate --rename-chrs /tmp/Qyl6m9GNFO/rename.map -Ov /«PKGBUILDDIR»/test/annotate.vcf | /«PKGBUILDDIR»/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /«PKGBUILDDIR»/bcftools annotate --rename-chrs /tmp/Qyl6m9GNFO/rename.map -Ob /«PKGBUILDDIR»/test/annotate.vcf | /«PKGBUILDDIR»/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -g -,. /tmp/Qyl6m9GNFO/convert.vcf.gz Gen file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 1 records skipped: 0/1/0/0 no-ALT/non-biallelic/filtered/duplicated .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g -,. Gen file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 1 records skipped: 0/1/0/0 no-ALT/non-biallelic/filtered/duplicated .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -g .,- /tmp/Qyl6m9GNFO/convert.vcf.gz Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g .,- Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -g -,. --tag PL /tmp/Qyl6m9GNFO/convert.vcf.gz Gen file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 1 records skipped: 0/1/0/0 no-ALT/non-biallelic/filtered/duplicated .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g -,. --tag PL Gen file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 1 records skipped: 0/1/0/0 no-ALT/non-biallelic/filtered/duplicated .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -g .,- --tag PL /tmp/Qyl6m9GNFO/convert.vcf.gz Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g .,- --tag PL Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -g -,. --vcf-ids /tmp/Qyl6m9GNFO/check.vcf.gz Gen file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 8 records skipped: 0/6/0/2 no-ALT/non-biallelic/filtered/duplicated .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/check.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g -,. --vcf-ids Gen file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 8 records skipped: 0/6/0/2 no-ALT/non-biallelic/filtered/duplicated .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -g .,- --vcf-ids /tmp/Qyl6m9GNFO/check.vcf.gz Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/check.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g .,- --vcf-ids Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -g -,. --chrom /tmp/Qyl6m9GNFO/check.vcf.gz Gen file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 8 records skipped: 0/6/0/2 no-ALT/non-biallelic/filtered/duplicated .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/check.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g -,. --chrom Gen file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 8 records skipped: 0/6/0/2 no-ALT/non-biallelic/filtered/duplicated .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -g .,- --chrom /tmp/Qyl6m9GNFO/check.vcf.gz Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/check.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g .,- --chrom Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -g -,. --chrom --vcf-ids /tmp/Qyl6m9GNFO/check.vcf.gz Gen file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 8 records skipped: 0/6/0/2 no-ALT/non-biallelic/filtered/duplicated .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/check.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g -,. --chrom --vcf-ids Gen file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 8 records skipped: 0/6/0/2 no-ALT/non-biallelic/filtered/duplicated .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -g .,- --chrom --vcf-ids /tmp/Qyl6m9GNFO/check.vcf.gz Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/check.vcf.gz | /«PKGBUILDDIR»/bcftools convert -g .,- --chrom --vcf-ids Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -h -,.,. /tmp/Qyl6m9GNFO/convert.vcf.gz Haps file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 1 records skipped: 0/1/0 no-ALT/non-biallelic/filtered .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -h -,.,. Haps file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 1 records skipped: 0/1/0 no-ALT/non-biallelic/filtered .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -h .,-,. /tmp/Qyl6m9GNFO/convert.vcf.gz Legend file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 1 records skipped: 0/1/0 no-ALT/non-biallelic/filtered .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -h .,-,. Legend file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 1 records skipped: 0/1/0 no-ALT/non-biallelic/filtered .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert -h .,.,- /tmp/Qyl6m9GNFO/convert.vcf.gz Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert -h .,.,- Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert --hapsample -,. /tmp/Qyl6m9GNFO/convert.vcf.gz Haps file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 1 records skipped: 0/1/0 no-ALT/non-biallelic/filtered .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert --hapsample -,. Haps file: - Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'. 1 records skipped: 0/1/0 no-ALT/non-biallelic/filtered .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools convert --hapsample .,- /tmp/Qyl6m9GNFO/convert.vcf.gz Sample file: - .. ok test_vcf_convert: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/convert.vcf.gz | /«PKGBUILDDIR»/bcftools convert --hapsample .,- Sample file: - .. ok test_vcf_convert_gvcf: /«PKGBUILDDIR»/bcftools convert --gvcf2vcf /tmp/Qyl6m9GNFO/convert.gvcf.vcf.gz | grep -v ^##bcftools .. ok test_vcf_convert_gvcf: /«PKGBUILDDIR»/bcftools view -Ob /tmp/Qyl6m9GNFO/convert.gvcf.vcf.gz | /«PKGBUILDDIR»/bcftools convert --gvcf2vcf | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /«PKGBUILDDIR»/bcftools convert -c ID,CHROM,POS,AA -s SAMPLE1 -f /«PKGBUILDDIR»/test/23andme.fa --tsv2vcf /«PKGBUILDDIR»/test/convert.23andme | grep -v ^##bcftools_ Rows total: 27 Rows skipped: 0 Missing GTs: 1 Hom RR: 14 Het RA: 7 Hom AA: 5 Het AA: 0 .. ok test_vcf_convert_tsv2vcf: /«PKGBUILDDIR»/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /«PKGBUILDDIR»/test/23andme.fa --tsv2vcf /«PKGBUILDDIR»/test/convert.23andme | /«PKGBUILDDIR»/bcftools view | grep -v ^##bcftools_ Rows total: 27 Rows skipped: 0 Missing GTs: 1 Hom RR: 14 Het RA: 7 Hom AA: 5 Het AA: 0 .. ok test_vcf_consensus: /«PKGBUILDDIR»/bcftools consensus /tmp/Qyl6m9GNFO/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -m /«PKGBUILDDIR»/test/consensus.tab About: Create consensus sequence by applying VCF variants to a reference fasta file. Usage: bcftools consensus [OPTIONS] Options: -f, --fasta-ref reference sequence in fasta format -H, --haplotype <1|2> apply variants for the given haplotype -i, --iupac-codes output variants in the form of IUPAC ambiguity codes -m, --mask replace regions with N -o, --output write output to a file [standard output] -c, --chain write a chain file for liftover -s, --sample apply variants of the given sample Examples: # Get the consensus for one region. The fasta header lines are then expected # in the form ">chr:from-to". samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz > out.fa Non-zero status 1 .. failed ... test_vcf_consensus_chain: /«PKGBUILDDIR»/bcftools consensus /tmp/Qyl6m9GNFO/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -m /«PKGBUILDDIR»/test/consensus.tab -c /tmp/Qyl6m9GNFO/consensus.1.chain.new > /dev/null; cat /tmp/Qyl6m9GNFO/consensus.1.chain.new About: Create consensus sequence by applying VCF variants to a reference fasta file. Usage: bcftools consensus [OPTIONS] Options: -f, --fasta-ref reference sequence in fasta format -H, --haplotype <1|2> apply variants for the given haplotype -i, --iupac-codes output variants in the form of IUPAC ambiguity codes -m, --mask replace regions with N -o, --output write output to a file [standard output] -c, --chain write a chain file for liftover -s, --sample apply variants of the given sample Examples: # Get the consensus for one region. The fasta header lines are then expected # in the form ">chr:from-to". samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz > out.fa cat: /tmp/Qyl6m9GNFO/consensus.1.chain.new: No such file or directory Non-zero status 1 .. failed ... test_vcf_consensus: /«PKGBUILDDIR»/bcftools consensus /tmp/Qyl6m9GNFO/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -H 1 -m /«PKGBUILDDIR»/test/consensus.tab About: Create consensus sequence by applying VCF variants to a reference fasta file. Usage: bcftools consensus [OPTIONS] Options: -f, --fasta-ref reference sequence in fasta format -H, --haplotype <1|2> apply variants for the given haplotype -i, --iupac-codes output variants in the form of IUPAC ambiguity codes -m, --mask replace regions with N -o, --output write output to a file [standard output] -c, --chain write a chain file for liftover -s, --sample apply variants of the given sample Examples: # Get the consensus for one region. The fasta header lines are then expected # in the form ">chr:from-to". samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz > out.fa Non-zero status 1 .. failed ... test_vcf_consensus_chain: /«PKGBUILDDIR»/bcftools consensus /tmp/Qyl6m9GNFO/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -H 1 -m /«PKGBUILDDIR»/test/consensus.tab -c /tmp/Qyl6m9GNFO/consensus.2.chain.new > /dev/null; cat /tmp/Qyl6m9GNFO/consensus.2.chain.new About: Create consensus sequence by applying VCF variants to a reference fasta file. Usage: bcftools consensus [OPTIONS] Options: -f, --fasta-ref reference sequence in fasta format -H, --haplotype <1|2> apply variants for the given haplotype -i, --iupac-codes output variants in the form of IUPAC ambiguity codes -m, --mask replace regions with N -o, --output write output to a file [standard output] -c, --chain write a chain file for liftover -s, --sample apply variants of the given sample Examples: # Get the consensus for one region. The fasta header lines are then expected # in the form ">chr:from-to". samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz > out.fa cat: /tmp/Qyl6m9GNFO/consensus.2.chain.new: No such file or directory Non-zero status 1 .. failed ... test_vcf_consensus: /«PKGBUILDDIR»/bcftools consensus /tmp/Qyl6m9GNFO/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -i -m /«PKGBUILDDIR»/test/consensus.tab About: Create consensus sequence by applying VCF variants to a reference fasta file. Usage: bcftools consensus [OPTIONS] Options: -f, --fasta-ref reference sequence in fasta format -H, --haplotype <1|2> apply variants for the given haplotype -i, --iupac-codes output variants in the form of IUPAC ambiguity codes -m, --mask replace regions with N -o, --output write output to a file [standard output] -c, --chain write a chain file for liftover -s, --sample apply variants of the given sample Examples: # Get the consensus for one region. The fasta header lines are then expected # in the form ">chr:from-to". samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz > out.fa Non-zero status 1 .. failed ... test_vcf_consensus_chain: /«PKGBUILDDIR»/bcftools consensus /tmp/Qyl6m9GNFO/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -i -m /«PKGBUILDDIR»/test/consensus.tab -c /tmp/Qyl6m9GNFO/consensus.3.chain.new > /dev/null; cat /tmp/Qyl6m9GNFO/consensus.3.chain.new About: Create consensus sequence by applying VCF variants to a reference fasta file. Usage: bcftools consensus [OPTIONS] Options: -f, --fasta-ref reference sequence in fasta format -H, --haplotype <1|2> apply variants for the given haplotype -i, --iupac-codes output variants in the form of IUPAC ambiguity codes -m, --mask replace regions with N -o, --output write output to a file [standard output] -c, --chain write a chain file for liftover -s, --sample apply variants of the given sample Examples: # Get the consensus for one region. The fasta header lines are then expected # in the form ">chr:from-to". samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz > out.fa cat: /tmp/Qyl6m9GNFO/consensus.3.chain.new: No such file or directory Non-zero status 1 .. failed ... test_vcf_consensus: /«PKGBUILDDIR»/bcftools consensus /tmp/Qyl6m9GNFO/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -H 1 About: Create consensus sequence by applying VCF variants to a reference fasta file. Usage: bcftools consensus [OPTIONS] Options: -f, --fasta-ref reference sequence in fasta format -H, --haplotype <1|2> apply variants for the given haplotype -i, --iupac-codes output variants in the form of IUPAC ambiguity codes -m, --mask replace regions with N -o, --output write output to a file [standard output] -c, --chain write a chain file for liftover -s, --sample apply variants of the given sample Examples: # Get the consensus for one region. The fasta header lines are then expected # in the form ">chr:from-to". samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz > out.fa Non-zero status 1 .. failed ... test_vcf_consensus_chain: /«PKGBUILDDIR»/bcftools consensus /tmp/Qyl6m9GNFO/consensus.vcf.gz -f /«PKGBUILDDIR»/test/consensus.fa -H 1 -c /tmp/Qyl6m9GNFO/consensus.4.chain.new > /dev/null; cat /tmp/Qyl6m9GNFO/consensus.4.chain.new About: Create consensus sequence by applying VCF variants to a reference fasta file. Usage: bcftools consensus [OPTIONS] Options: -f, --fasta-ref reference sequence in fasta format -H, --haplotype <1|2> apply variants for the given haplotype -i, --iupac-codes output variants in the form of IUPAC ambiguity codes -m, --mask replace regions with N -o, --output write output to a file [standard output] -c, --chain write a chain file for liftover -s, --sample apply variants of the given sample Examples: # Get the consensus for one region. The fasta header lines are then expected # in the form ">chr:from-to". samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz > out.fa cat: /tmp/Qyl6m9GNFO/consensus.4.chain.new: No such file or directory Non-zero status 1 .. failed ... Number of tests: total .. 316 passed .. 308 failed .. 8 Makefile:93: recipe for target 'test' failed make[1]: *** [test] Error 1 make[1]: Leaving directory '/«PKGBUILDDIR»' dh_auto_test: make -j8 test returned exit code 2 make: *** [build-arch] Error 2 debian/rules:15: recipe for target 'build-arch' failed dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20160627-0348 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: arm64 Build-Space: 10084 Build-Time: 21 Distribution: xenial Fail-Stage: build Host Architecture: arm64 Install-Time: 55 Job: bcftools_1.2-2.dsc Machine Architecture: arm64 Package: bcftools Package-Time: 78 Source-Version: 1.2-2 Space: 10084 Status: attempted Version: 1.2-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20160627-0348 Build needed 00:01:18, 10084k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-10059195'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-10059195/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-10059195'] Unmounting chroot for build PACKAGEBUILD-10059195... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-10059195'] Removing build PACKAGEBUILD-10059195