RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-005 4.4.0-81-generic #104-Ubuntu SMP Wed Jun 14 08:22:02 UTC 2017 aarch64 Buildd toolchain package versions: launchpad-buildd_144 python-lpbuildd_144 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.1 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.14. Syncing the system clock with the buildd NTP service... 26 Jun 07:25:05 ntpdate[2206]: adjust time server 10.211.37.1 offset -0.035483 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8886985', '/home/buildd/filecache-default/b3be73ab5ae7c15f478bfb6b61c08aecabde888d'] Unpacking chroot for build PACKAGEBUILD-8886985 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8886985'] Mounting chroot for build PACKAGEBUILD-8886985 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8886985', 'deb http://ftpmaster.internal/ubuntu xenial main universe', 'deb http://ftpmaster.internal/ubuntu xenial-security main universe', 'deb http://ftpmaster.internal/ubuntu xenial-updates main universe', 'deb http://ftpmaster.internal/ubuntu xenial-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-8886985 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8886985', 'armhf'] Updating debian chroot for build PACKAGEBUILD-8886985 Hit:1 http://ftpmaster.internal/ubuntu xenial InRelease Get:2 http://ftpmaster.internal/ubuntu xenial-security InRelease [102 kB] Get:3 http://ftpmaster.internal/ubuntu xenial-updates InRelease [102 kB] Get:4 http://ftpmaster.internal/ubuntu xenial-proposed InRelease [253 kB] Get:5 http://ftpmaster.internal/ubuntu xenial-security/main armhf Packages [245 kB] Get:6 http://ftpmaster.internal/ubuntu xenial-security/main Translation-en [124 kB] Get:7 http://ftpmaster.internal/ubuntu xenial-security/universe armhf Packages [136 kB] Get:8 http://ftpmaster.internal/ubuntu xenial-security/universe Translation-en [72.2 kB] Get:9 http://ftpmaster.internal/ubuntu xenial-updates/main armhf Packages [506 kB] Get:10 http://ftpmaster.internal/ubuntu xenial-updates/main Translation-en [229 kB] Get:11 http://ftpmaster.internal/ubuntu xenial-updates/universe armhf Packages [444 kB] Get:12 http://ftpmaster.internal/ubuntu xenial-updates/universe Translation-en [193 kB] Get:13 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf Packages [99.7 kB] Get:14 http://ftpmaster.internal/ubuntu xenial-proposed/main Translation-en [44.3 kB] Get:15 http://ftpmaster.internal/ubuntu xenial-proposed/universe armhf Packages [38.2 kB] Get:16 http://ftpmaster.internal/ubuntu xenial-proposed/universe Translation-en [20.8 kB] Fetched 2610 kB in 2s (1253 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt apt-transport-https base-files bash binutils bsdutils coreutils cpp-5 dpkg dpkg-dev g++-5 gcc-5 gcc-5-base gnupg gpgv grep init init-system-helpers libapparmor1 libapt-pkg5.0 libasan2 libatomic1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcurl3-gnutls libdbus-1-3 libdpkg-perl libfdisk1 libgcc-5-dev libgcrypt20 libgnutls30 libgomp1 libgssapi-krb5-2 libhogweed4 libidn11 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libmount1 libnettle6 libp11-kit0 libprocps4 librtmp1 libsmartcols1 libssl1.0.0 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libuuid1 linux-libc-dev login lsb-base mount multiarch-support openssl passwd procps systemd systemd-sysv tar tzdata util-linux zlib1g 71 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 42.8 MB of archives. After this operation, 190 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu xenial-updates/main armhf base-files armhf 9.4ubuntu4.4 [68.6 kB] Get:2 http://ftpmaster.internal/ubuntu xenial-security/main armhf bash armhf 4.3-14ubuntu1.2 [503 kB] Get:3 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf bsdutils armhf 1:2.27.1-6ubuntu3.3 [49.4 kB] Get:4 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf coreutils armhf 8.25-2ubuntu3~16.04 [1075 kB] Get:5 http://ftpmaster.internal/ubuntu xenial-updates/main armhf dpkg armhf 1.18.4ubuntu1.2 [1987 kB] Get:6 http://ftpmaster.internal/ubuntu xenial-updates/main armhf grep armhf 2.25-1~16.04.1 [141 kB] Get:7 http://ftpmaster.internal/ubuntu xenial-updates/main armhf init-system-helpers all 1.29ubuntu4 [32.3 kB] Get:8 http://ftpmaster.internal/ubuntu xenial-updates/main armhf init armhf 1.29ubuntu4 [4612 B] Get:9 http://ftpmaster.internal/ubuntu xenial-security/main armhf login armhf 1:4.2-3.1ubuntu5.3 [302 kB] Get:10 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libsystemd0 armhf 229-4ubuntu17 [187 kB] Get:11 http://ftpmaster.internal/ubuntu xenial-updates/main armhf systemd armhf 229-4ubuntu17 [3215 kB] Get:12 http://ftpmaster.internal/ubuntu xenial-security/main armhf libc6-dev armhf 2.23-0ubuntu9 [1643 kB] Get:13 http://ftpmaster.internal/ubuntu xenial-security/main armhf libc-dev-bin armhf 2.23-0ubuntu9 [59.2 kB] Get:14 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf linux-libc-dev armhf 4.4.0-82.105 [822 kB] Get:15 http://ftpmaster.internal/ubuntu xenial-security/main armhf libc6 armhf 2.23-0ubuntu9 [2143 kB] Get:16 http://ftpmaster.internal/ubuntu xenial-security/main armhf libapparmor1 armhf 2.10.95-0ubuntu2.6 [27.9 kB] Get:17 http://ftpmaster.internal/ubuntu xenial-security/main armhf passwd armhf 1:4.2-3.1ubuntu5.3 [746 kB] Get:18 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf libuuid1 armhf 2.27.1-6ubuntu3.3 [15.1 kB] Get:19 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf libblkid1 armhf 2.27.1-6ubuntu3.3 [94.7 kB] Get:20 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf libmount1 armhf 2.27.1-6ubuntu3.3 [101 kB] Get:21 http://ftpmaster.internal/ubuntu xenial-updates/main armhf lsb-base all 9.20160110ubuntu0.2 [13.7 kB] Get:22 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf util-linux armhf 2.27.1-6ubuntu3.3 [795 kB] Get:23 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf mount armhf 2.27.1-6ubuntu3.3 [117 kB] Get:24 http://ftpmaster.internal/ubuntu xenial-security/main armhf tar armhf 1.28-2.1ubuntu0.1 [181 kB] Get:25 http://ftpmaster.internal/ubuntu xenial-security/main armhf libc-bin armhf 2.23-0ubuntu9 [486 kB] Get:26 http://ftpmaster.internal/ubuntu xenial-security/main armhf libubsan0 armhf 5.4.0-6ubuntu1~16.04.4 [84.4 kB] Get:27 http://ftpmaster.internal/ubuntu xenial-security/main armhf libgomp1 armhf 5.4.0-6ubuntu1~16.04.4 [49.9 kB] Get:28 http://ftpmaster.internal/ubuntu xenial-security/main armhf libatomic1 armhf 5.4.0-6ubuntu1~16.04.4 [6018 B] Get:29 http://ftpmaster.internal/ubuntu xenial-security/main armhf libasan2 armhf 5.4.0-6ubuntu1~16.04.4 [240 kB] Get:30 http://ftpmaster.internal/ubuntu xenial-updates/main armhf zlib1g armhf 1:1.2.8.dfsg-2ubuntu4.1 [45.4 kB] Get:31 http://ftpmaster.internal/ubuntu xenial-security/main armhf g++-5 armhf 5.4.0-6ubuntu1~16.04.4 [5280 kB] Get:32 http://ftpmaster.internal/ubuntu xenial-security/main armhf gcc-5 armhf 5.4.0-6ubuntu1~16.04.4 [5548 kB] Get:33 http://ftpmaster.internal/ubuntu xenial-security/main armhf cpp-5 armhf 5.4.0-6ubuntu1~16.04.4 [4913 kB] Get:34 http://ftpmaster.internal/ubuntu xenial-security/main armhf libcc1-0 armhf 5.4.0-6ubuntu1~16.04.4 [25.8 kB] Get:35 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf binutils armhf 2.26.1-1ubuntu1~16.04.4 [2342 kB] Get:36 http://ftpmaster.internal/ubuntu xenial-security/main armhf libstdc++-5-dev armhf 5.4.0-6ubuntu1~16.04.4 [1467 kB] Get:37 http://ftpmaster.internal/ubuntu xenial-security/main armhf libgcc-5-dev armhf 5.4.0-6ubuntu1~16.04.4 [470 kB] Get:38 http://ftpmaster.internal/ubuntu xenial-security/main armhf gcc-5-base armhf 5.4.0-6ubuntu1~16.04.4 [16.9 kB] Get:39 http://ftpmaster.internal/ubuntu xenial-security/main armhf libstdc++6 armhf 5.4.0-6ubuntu1~16.04.4 [351 kB] Get:40 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libapt-pkg5.0 armhf 1.2.20 [651 kB] Get:41 http://ftpmaster.internal/ubuntu xenial-security/main armhf gpgv armhf 1.4.20-1ubuntu3.1 [136 kB] Get:42 http://ftpmaster.internal/ubuntu xenial-security/main armhf gnupg armhf 1.4.20-1ubuntu3.1 [563 kB] Get:43 http://ftpmaster.internal/ubuntu xenial-updates/main armhf apt armhf 1.2.20 [1014 kB] Get:44 http://ftpmaster.internal/ubuntu xenial-updates/main armhf systemd-sysv armhf 229-4ubuntu17 [12.8 kB] Get:45 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf libfdisk1 armhf 2.27.1-6ubuntu3.3 [127 kB] Get:46 http://ftpmaster.internal/ubuntu xenial-security/main armhf libgcrypt20 armhf 1.6.5-2ubuntu0.2 [306 kB] Get:47 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf libsmartcols1 armhf 2.27.1-6ubuntu3.3 [55.4 kB] Get:48 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libudev1 armhf 229-4ubuntu17 [50.0 kB] Get:49 http://ftpmaster.internal/ubuntu xenial-security/main armhf multiarch-support armhf 2.23-0ubuntu9 [6826 B] Get:50 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libprocps4 armhf 2:3.3.10-4ubuntu2.3 [29.8 kB] Get:51 http://ftpmaster.internal/ubuntu xenial-updates/main armhf procps armhf 2:3.3.10-4ubuntu2.3 [208 kB] Get:52 http://ftpmaster.internal/ubuntu xenial-security/main armhf tzdata all 2016j-0ubuntu0.16.04 [168 kB] Get:53 http://ftpmaster.internal/ubuntu xenial-security/main armhf libhogweed4 armhf 3.2-1ubuntu0.16.04.1 [126 kB] Get:54 http://ftpmaster.internal/ubuntu xenial-security/main armhf libnettle6 armhf 3.2-1ubuntu0.16.04.1 [111 kB] Get:55 http://ftpmaster.internal/ubuntu xenial-security/main armhf libidn11 armhf 1.32-3ubuntu1.1 [42.7 kB] Get:56 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libp11-kit0 armhf 0.23.2-5~ubuntu16.04.1 [91.0 kB] Get:57 http://ftpmaster.internal/ubuntu xenial-security/main armhf libtasn1-6 armhf 4.7-3ubuntu0.16.04.2 [37.6 kB] Get:58 http://ftpmaster.internal/ubuntu xenial-security/main armhf libgnutls30 armhf 3.4.10-4ubuntu1.3 [486 kB] Get:59 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libssl1.0.0 armhf 1.0.2g-1ubuntu4.8 [712 kB] Get:60 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libgssapi-krb5-2 armhf 1.13.2+dfsg-5ubuntu2 [98.7 kB] Get:61 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libkrb5-3 armhf 1.13.2+dfsg-5ubuntu2 [230 kB] Get:62 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libkrb5support0 armhf 1.13.2+dfsg-5ubuntu2 [27.2 kB] Get:63 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libk5crypto3 armhf 1.13.2+dfsg-5ubuntu2 [77.5 kB] Get:64 http://ftpmaster.internal/ubuntu xenial-security/main armhf libldap-2.4-2 armhf 2.4.42+dfsg-2ubuntu3.2 [138 kB] Get:65 http://ftpmaster.internal/ubuntu xenial-security/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d-1ubuntu0.1 [49.4 kB] Get:66 http://ftpmaster.internal/ubuntu xenial-security/main armhf libcurl3-gnutls armhf 7.47.0-1ubuntu2.2 [159 kB] Get:67 http://ftpmaster.internal/ubuntu xenial-updates/main armhf apt-transport-https armhf 1.2.20 [23.3 kB] Get:68 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libdbus-1-3 armhf 1.10.6-1ubuntu3.3 [141 kB] Get:69 http://ftpmaster.internal/ubuntu xenial-updates/main armhf openssl armhf 1.0.2g-1ubuntu4.8 [485 kB] Get:70 http://ftpmaster.internal/ubuntu xenial-updates/main armhf dpkg-dev all 1.18.4ubuntu1.2 [584 kB] Get:71 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libdpkg-perl all 1.18.4ubuntu1.2 [195 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 42.8 MB in 1s (25.1 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Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libapparmor1:armhf (2.10.95-0ubuntu2.6) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (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 ... 11919 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.2-3.1ubuntu5.3_armhf.deb ... Unpacking passwd (1:4.2-3.1ubuntu5.3) over (1:4.2-3.1ubuntu5) ... Setting up passwd (1:4.2-3.1ubuntu5.3) ... (Reading database ... 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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d-1ubuntu0.1) over (2.4+20151223.gitfa8646d-1build1) ... Preparing to unpack .../libcurl3-gnutls_7.47.0-1ubuntu2.2_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.47.0-1ubuntu2.2) over (7.47.0-1ubuntu2) ... Preparing to unpack .../apt-transport-https_1.2.20_armhf.deb ... Unpacking apt-transport-https (1.2.20) over (1.2.10ubuntu1) ... Preparing to unpack .../libdbus-1-3_1.10.6-1ubuntu3.3_armhf.deb ... Unpacking libdbus-1-3:armhf (1.10.6-1ubuntu3.3) over (1.10.6-1ubuntu3) ... Preparing to unpack .../openssl_1.0.2g-1ubuntu4.8_armhf.deb ... Unpacking openssl (1.0.2g-1ubuntu4.8) over (1.0.2g-1ubuntu4) ... Preparing to unpack .../dpkg-dev_1.18.4ubuntu1.2_all.deb ... Unpacking dpkg-dev (1.18.4ubuntu1.2) over (1.18.4ubuntu1) ... Preparing to unpack .../libdpkg-perl_1.18.4ubuntu1.2_all.deb ... Unpacking libdpkg-perl (1.18.4ubuntu1.2) over (1.18.4ubuntu1) ... Processing triggers for libc-bin (2.23-0ubuntu9) ... Processing triggers for systemd (229-4ubuntu17) ... Setting up libc-dev-bin (2.23-0ubuntu9) ... Setting up linux-libc-dev:armhf (4.4.0-82.105) ... Setting up libc6-dev:armhf (2.23-0ubuntu9) ... Setting up libubsan0:armhf (5.4.0-6ubuntu1~16.04.4) ... Setting up libgomp1:armhf (5.4.0-6ubuntu1~16.04.4) ... Setting up libatomic1:armhf (5.4.0-6ubuntu1~16.04.4) ... Setting up libasan2:armhf (5.4.0-6ubuntu1~16.04.4) ... Setting up cpp-5 (5.4.0-6ubuntu1~16.04.4) ... Setting up libcc1-0:armhf (5.4.0-6ubuntu1~16.04.4) ... Setting up binutils (2.26.1-1ubuntu1~16.04.4) ... Setting up libgcc-5-dev:armhf (5.4.0-6ubuntu1~16.04.4) ... Setting up gcc-5 (5.4.0-6ubuntu1~16.04.4) ... Setting up libstdc++-5-dev:armhf (5.4.0-6ubuntu1~16.04.4) ... Setting up g++-5 (5.4.0-6ubuntu1~16.04.4) ... Setting up libprocps4:armhf (2:3.3.10-4ubuntu2.3) ... Setting up procps (2:3.3.10-4ubuntu2.3) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Setting up tzdata (2016j-0ubuntu0.16.04) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jun 26 07:25:37 UTC 2017. Universal Time is now: Mon Jun 26 07:25:37 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libnettle6:armhf (3.2-1ubuntu0.16.04.1) ... Setting up libhogweed4:armhf (3.2-1ubuntu0.16.04.1) ... Setting up libidn11:armhf (1.32-3ubuntu1.1) ... Setting up libp11-kit0:armhf (0.23.2-5~ubuntu16.04.1) ... Setting up libtasn1-6:armhf (4.7-3ubuntu0.16.04.2) ... Setting up libgnutls30:armhf (3.4.10-4ubuntu1.3) ... Setting up libssl1.0.0:armhf (1.0.2g-1ubuntu4.8) ... Setting up libkrb5support0:armhf (1.13.2+dfsg-5ubuntu2) ... Setting up libk5crypto3:armhf (1.13.2+dfsg-5ubuntu2) ... Setting up libkrb5-3:armhf (1.13.2+dfsg-5ubuntu2) ... Setting up libgssapi-krb5-2:armhf (1.13.2+dfsg-5ubuntu2) ... Setting up libldap-2.4-2:armhf (2.4.42+dfsg-2ubuntu3.2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d-1ubuntu0.1) ... Setting up libcurl3-gnutls:armhf (7.47.0-1ubuntu2.2) ... Setting up apt-transport-https (1.2.20) ... Setting up libdbus-1-3:armhf (1.10.6-1ubuntu3.3) ... Setting up openssl (1.0.2g-1ubuntu4.8) ... Setting up libdpkg-perl (1.18.4ubuntu1.2) ... Setting up dpkg-dev (1.18.4ubuntu1.2) ... Processing triggers for libc-bin (2.23-0ubuntu9) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-8886985', 'armhf', 'xenial-proposed', '-c', 'chroot:autobuild', '--arch=armhf', '--dist=xenial-proposed', '--purge=never', '--nolog', 'bcftools_1.2-2.dsc'] Initiating build PACKAGEBUILD-8886985 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-81-generic #104-Ubuntu SMP Wed Jun 14 08:22:02 UTC 2017 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-arm64-005.buildd +==============================================================================+ | bcftools 1.2-2 (armhf) 26 Jun 2017 07:25 | +==============================================================================+ Package: bcftools Version: 1.2-2 Source Version: 1.2-2 Distribution: xenial-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/bcftools-riWSx7/bcftools-1.2' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-riWSx7' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8886985/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | 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 '/<>/resolver-Ys4Y1E/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-Ys4Y1E/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Ys4Y1E/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Ys4Y1E/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Ys4Y1E/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-Ys4Y1E/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (112 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 772 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Ys4Y1E/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 772 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 ... 11934 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), zlib1g-dev, libhts-dev (>= 1.2.1), libgsl-dev, tabix, libio-pty-perl Filtered Build-Depends: 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 '/<>/resolver-GHzQpm/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. Ign:1 copy:/<>/resolver-GHzQpm/apt_archive ./ InRelease Get:2 copy:/<>/resolver-GHzQpm/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-GHzQpm/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-GHzQpm/apt_archive ./ Sources [247 B] Get:5 copy:/<>/resolver-GHzQpm/apt_archive ./ Packages [566 B] Fetched 2932 B in 0s (145 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install bcftools build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: 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 16.1 MB of archives. After this operation, 58.5 MB of additional disk space will be used. Get:1 copy:/<>/resolver-GHzQpm/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [810 B] Get:2 http://ftpmaster.internal/ubuntu xenial/main armhf groff-base armhf 1.22.3-7 [1023 kB] Get:3 http://ftpmaster.internal/ubuntu xenial/main armhf bsdmainutils armhf 9.0.6ubuntu3 [169 kB] Get:4 http://ftpmaster.internal/ubuntu xenial/main armhf libpipeline1 armhf 1.4.1-2 [21.0 kB] Get:5 http://ftpmaster.internal/ubuntu xenial/main armhf man-db armhf 2.7.5-1 [836 kB] Get:6 http://ftpmaster.internal/ubuntu xenial/main armhf libunistring0 armhf 0.9.3-5.2ubuntu1 [250 kB] Get:7 http://ftpmaster.internal/ubuntu xenial/main armhf libmagic1 armhf 1:5.25-2ubuntu1 [211 kB] Get:8 http://ftpmaster.internal/ubuntu xenial/main armhf file armhf 1:5.25-2ubuntu1 [20.9 kB] Get:9 http://ftpmaster.internal/ubuntu xenial/main armhf libasprintf0v5 armhf 0.19.7-2ubuntu3 [6158 B] Get:10 http://ftpmaster.internal/ubuntu xenial/main armhf gettext-base armhf 0.19.7-2ubuntu3 [44.5 kB] Get:11 http://ftpmaster.internal/ubuntu xenial-updates/main armhf libglib2.0-0 armhf 2.48.2-0ubuntu1 [979 kB] Get:12 http://ftpmaster.internal/ubuntu xenial-security/main armhf libicu55 armhf 55.1-7ubuntu0.2 [7403 kB] Get:13 http://ftpmaster.internal/ubuntu xenial-security/main armhf libxml2 armhf 2.9.3+dfsg1-1ubuntu0.2 [605 kB] Get:14 http://ftpmaster.internal/ubuntu xenial/main armhf autotools-dev all 20150820.1 [39.8 kB] Get:15 http://ftpmaster.internal/ubuntu xenial/main armhf libcroco3 armhf 0.6.11-1 [70.0 kB] Get:16 http://ftpmaster.internal/ubuntu xenial/main armhf gettext armhf 0.19.7-2ubuntu3 [1013 kB] Get:17 http://ftpmaster.internal/ubuntu xenial/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:18 http://ftpmaster.internal/ubuntu xenial/main armhf po-debconf all 1.0.19 [234 kB] Get:19 http://ftpmaster.internal/ubuntu xenial/main armhf libarchive-zip-perl all 1.56-2 [84.1 kB] Get:20 http://ftpmaster.internal/ubuntu xenial/main armhf libfile-stripnondeterminism-perl all 0.015-1 [10.3 kB] Get:21 http://ftpmaster.internal/ubuntu xenial/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:22 http://ftpmaster.internal/ubuntu xenial/main armhf dh-strip-nondeterminism all 0.015-1 [4864 B] Get:23 http://ftpmaster.internal/ubuntu xenial/main armhf debhelper all 9.20160115ubuntu3 [739 kB] Get:24 http://ftpmaster.internal/ubuntu xenial/main armhf libgsl2 armhf 2.1+dfsg-2 [687 kB] Get:25 http://ftpmaster.internal/ubuntu xenial/main armhf libgsl-dev armhf 2.1+dfsg-2 [823 kB] Get:26 http://ftpmaster.internal/ubuntu xenial/universe armhf libhts1 armhf 1.2.1-2ubuntu1 [194 kB] Get:27 http://ftpmaster.internal/ubuntu xenial/universe armhf libhts-dev armhf 1.2.1-2ubuntu1 [245 kB] Get:28 http://ftpmaster.internal/ubuntu xenial/main armhf libio-pty-perl armhf 1:1.08-1.1build1 [29.5 kB] Get:29 http://ftpmaster.internal/ubuntu xenial/universe armhf tabix armhf 1.2.1-2ubuntu1 [184 kB] Get:30 http://ftpmaster.internal/ubuntu xenial-updates/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2ubuntu4.1 [161 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.1 MB in 4s (3744 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 ... 11934 files and directories currently installed.) Preparing to unpack .../groff-base_1.22.3-7_armhf.deb ... Unpacking groff-base (1.22.3-7) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu3_armhf.deb ... Unpacking bsdmainutils (9.0.6ubuntu3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../libpipeline1_1.4.1-2_armhf.deb ... 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Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1build1_armhf.deb ... Unpacking libio-pty-perl (1:1.08-1.1build1) ... Selecting previously unselected package tabix. Preparing to unpack .../tabix_1.2.1-2ubuntu1_armhf.deb ... Unpacking tabix (1.2.1-2ubuntu1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2ubuntu4.1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2ubuntu4.1) ... Selecting previously unselected package sbuild-build-depends-bcftools-dummy. Preparing to unpack .../sbuild-build-depends-bcftools-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.23-0ubuntu9) ... 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:armhf (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:armhf (0.9.3-5.2ubuntu1) ... Setting up libmagic1:armhf (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up libasprintf0v5:armhf (0.19.7-2ubuntu3) ... Setting up gettext-base (0.19.7-2ubuntu3) ... Setting up libglib2.0-0:armhf (2.48.2-0ubuntu1) ... No schema files found: doing nothing. Setting up libicu55:armhf (55.1-7ubuntu0.2) ... Setting up libxml2:armhf (2.9.3+dfsg1-1ubuntu0.2) ... Setting up autotools-dev (20150820.1) ... Setting up libcroco3:armhf (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:armhf (2.1+dfsg-2) ... Setting up libgsl-dev (2.1+dfsg-2) ... Setting up libhts1:armhf (1.2.1-2ubuntu1) ... Setting up libhts-dev:armhf (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:armhf (1:1.2.8.dfsg-2ubuntu4.1) ... 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 (2.23-0ubuntu9) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-81-generic arm64 (armv7l) Toolchain package versions: binutils_2.26.1-1ubuntu1~16.04.4 dpkg-dev_1.18.4ubuntu1.2 g++-5_5.4.0-6ubuntu1~16.04.4 gcc-5_5.4.0-6ubuntu1~16.04.4 libc6-dev_2.23-0ubuntu9 libstdc++-5-dev_5.4.0-6ubuntu1~16.04.4 libstdc++6_5.4.0-6ubuntu1~16.04.4 linux-libc-dev_4.4.0-82.105 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.2.20 apt-transport-https_1.2.20 autotools-dev_20150820.1 base-files_9.4ubuntu4.4 base-passwd_3.5.39 bash_4.3-14ubuntu1.2 binutils_2.26.1-1ubuntu1~16.04.4 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.27.1-6ubuntu3.3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20160104ubuntu1 coreutils_8.25-2ubuntu3~16.04 cpp_4:5.3.1-1ubuntu1 cpp-5_5.4.0-6ubuntu1~16.04.4 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_1.18.4ubuntu1.2 dpkg-dev_1.18.4ubuntu1.2 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_5.4.0-6ubuntu1~16.04.4 gcc_4:5.3.1-1ubuntu1 gcc-5_5.4.0-6ubuntu1~16.04.4 gcc-5-base_5.4.0-6ubuntu1~16.04.4 gcc-6-base_6.0.1-0ubuntu1 gettext_0.19.7-2ubuntu3 gettext-base_0.19.7-2ubuntu3 gnupg_1.4.20-1ubuntu3.1 gpgv_1.4.20-1ubuntu3.1 grep_2.25-1~16.04.1 groff-base_1.22.3-7 gzip_1.6-4ubuntu1 hostname_3.16ubuntu2 init_1.29ubuntu4 init-system-helpers_1.29ubuntu4 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-0ubuntu2.6 libapt-pkg5.0_1.2.20 libarchive-zip-perl_1.56-2 libasan2_5.4.0-6ubuntu1~16.04.4 libasn1-8-heimdal_1.7~git20150920+dfsg-4ubuntu1 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systemd_229-4ubuntu17 systemd-sysv_229-4ubuntu17 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.3ubuntu2 tabix_1.2.1-2ubuntu1 tar_1.28-2.1ubuntu0.1 tzdata_2016j-0ubuntu0.16.04 ubuntu-keyring_2012.05.19 util-linux_2.27.1-6ubuntu3.3 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4.1 zlib1g-dev_1:1.2.8.dfsg-2ubuntu4.1 +------------------------------------------------------------------------------+ | 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 ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=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=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && '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 armhf fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel make -j4 distclean make[1]: Entering directory '/<>' 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 '/<>' 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 -j4 make[1]: Entering directory '/<>' 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 '/<>' dh_auto_test -a -O--parallel make -j4 test make[1]: Entering directory '/<>' ./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/WKBfuOD9oT/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/WKBfuOD9oT/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: /usr/bin/tabix /tmp/WKBfuOD9oT/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/WKBfuOD9oT/merge.a.bcf 1:3000151-3000151 .. ok test_tabix: /usr/bin/tabix /tmp/WKBfuOD9oT/large_chrom_tbi_limit.vcf.gz chr11:1-536870912 .. ok test_tabix: /<>/bcftools view -H /tmp/WKBfuOD9oT/large_chrom_tbi_limit.bcf chr11:1-536870912 .. ok test_index: /<>/bcftools view -H /tmp/WKBfuOD9oT/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/WKBfuOD9oT/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/WKBfuOD9oT/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/WKBfuOD9oT/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/WKBfuOD9oT/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/WKBfuOD9oT/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/WKBfuOD9oT/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/WKBfuOD9oT/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/WKBfuOD9oT/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/WKBfuOD9oT/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/WKBfuOD9oT/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/WKBfuOD9oT/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/WKBfuOD9oT/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/WKBfuOD9oT/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/WKBfuOD9oT/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/WKBfuOD9oT/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/WKBfuOD9oT/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/check.vcf.gz | /<>/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/WKBfuOD9oT/stats.a.vcf.gz /tmp/WKBfuOD9oT/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/WKBfuOD9oT/isec.a.vcf.gz /tmp/WKBfuOD9oT/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/WKBfuOD9oT/isec.a.vcf.gz /tmp/WKBfuOD9oT/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/WKBfuOD9oT/isec.a.vcf.gz /tmp/WKBfuOD9oT/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/WKBfuOD9oT/isec.a.vcf.gz /tmp/WKBfuOD9oT/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/WKBfuOD9oT/isec.a.vcf.gz /tmp/WKBfuOD9oT/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/WKBfuOD9oT/isec.a.vcf.gz /tmp/WKBfuOD9oT/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/WKBfuOD9oT/isec.a.vcf.gz /tmp/WKBfuOD9oT/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/WKBfuOD9oT/isec.a.vcf.gz /tmp/WKBfuOD9oT/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/WKBfuOD9oT/isec.a.vcf.gz /tmp/WKBfuOD9oT/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/WKBfuOD9oT/isec.a.vcf.gz /tmp/WKBfuOD9oT/isec.b.vcf.gz Note: -w option not given, printing list of sites... .. ok test_vcf_isec2: /<>/bcftools isec -T /tmp/WKBfuOD9oT/isec.tab.gz /tmp/WKBfuOD9oT/isec.a.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/WKBfuOD9oT/isec.tab.gz /tmp/WKBfuOD9oT/isec.a.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --force-samples /tmp/WKBfuOD9oT/merge.a.vcf.gz /tmp/WKBfuOD9oT/merge.b.vcf.gz /tmp/WKBfuOD9oT/merge.c.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/WKBfuOD9oT/merge.a.vcf.gz /tmp/WKBfuOD9oT/merge.b.vcf.gz /tmp/WKBfuOD9oT/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --force-samples -m none /tmp/WKBfuOD9oT/merge.2.a.vcf.gz /tmp/WKBfuOD9oT/merge.2.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m none /tmp/WKBfuOD9oT/merge.2.a.vcf.gz /tmp/WKBfuOD9oT/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --force-samples -m both /tmp/WKBfuOD9oT/merge.2.a.vcf.gz /tmp/WKBfuOD9oT/merge.2.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m both /tmp/WKBfuOD9oT/merge.2.a.vcf.gz /tmp/WKBfuOD9oT/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --force-samples -m all /tmp/WKBfuOD9oT/merge.2.a.vcf.gz /tmp/WKBfuOD9oT/merge.2.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m all /tmp/WKBfuOD9oT/merge.2.a.vcf.gz /tmp/WKBfuOD9oT/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --force-samples -i TR:sum,TA:sum,TG:sum /tmp/WKBfuOD9oT/merge.3.a.vcf.gz /tmp/WKBfuOD9oT/merge.3.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/WKBfuOD9oT/merge.3.a.vcf.gz /tmp/WKBfuOD9oT/merge.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --force-samples -m id /tmp/WKBfuOD9oT/merge.4.a.vcf.gz /tmp/WKBfuOD9oT/merge.4.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m id /tmp/WKBfuOD9oT/merge.4.a.vcf.gz /tmp/WKBfuOD9oT/merge.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/WKBfuOD9oT/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/WKBfuOD9oT/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/view.filter.vcf.gz | /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /<>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/WKBfuOD9oT/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/view.filter.vcf.gz | /<>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/WKBfuOD9oT/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/WKBfuOD9oT/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/WKBfuOD9oT/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' /tmp/WKBfuOD9oT/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/WKBfuOD9oT/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' /tmp/WKBfuOD9oT/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' .. ok test_vcf_query: /<>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' /tmp/WKBfuOD9oT/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.vcf.gz | /<>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' .. ok test_vcf_query: /<>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/WKBfuOD9oT/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.vcf.gz | /<>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /<>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/WKBfuOD9oT/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.vcf.gz | /<>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' /tmp/WKBfuOD9oT/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.vcf.gz | /<>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' .. ok test_vcf_query: /<>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/WKBfuOD9oT/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/view.filter.vcf.gz | /<>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/WKBfuOD9oT/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/WKBfuOD9oT/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/WKBfuOD9oT/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/WKBfuOD9oT/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /<>/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/WKBfuOD9oT/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/view.vectors.vcf.gz | /<>/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' /tmp/WKBfuOD9oT/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.filter.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' /tmp/WKBfuOD9oT/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.filter.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' /tmp/WKBfuOD9oT/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.filter.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' /tmp/WKBfuOD9oT/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.filter.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/WKBfuOD9oT/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/query.2.vcf.gz | /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_norm: /<>/bcftools norm -f /<>/test/norm.fa /tmp/WKBfuOD9oT/norm.vcf.gz | grep -v ^##bcftools_ Lines total/modified/skipped: 21/13/0 .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/WKBfuOD9oT/norm.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ Lines total/modified/skipped: 21/13/0 .. ok test_vcf_norm: /<>/bcftools norm -m- /tmp/WKBfuOD9oT/norm.split.vcf.gz | grep -v ^##bcftools_ Lines total/modified/skipped: 18/0/0 .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/WKBfuOD9oT/norm.split.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ Lines total/modified/skipped: 18/0/0 .. ok test_vcf_norm: /<>/bcftools norm -m+ /tmp/WKBfuOD9oT/norm.merge.vcf.gz | grep -v ^##bcftools_ Lines total/modified/skipped: 26/0/0 .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/WKBfuOD9oT/norm.merge.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ Lines total/modified/skipped: 26/0/0 .. ok test_vcf_norm: /<>/bcftools norm -m+ -s /tmp/WKBfuOD9oT/norm.merge.vcf.gz | grep -v ^##bcftools_ Lines total/modified/skipped: 26/0/0 .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ -s /tmp/WKBfuOD9oT/norm.merge.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ Lines total/modified/skipped: 26/0/0 .. ok test_vcf_view: /<>/bcftools view -aUc1 -C1 -s NA00002 -v snps /tmp/WKBfuOD9oT/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/WKBfuOD9oT/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -f PASS -Xks NA00003 /tmp/WKBfuOD9oT/view.vcf.gz -r20,Y | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/WKBfuOD9oT/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -xs NA00003 /tmp/WKBfuOD9oT/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/WKBfuOD9oT/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/WKBfuOD9oT/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/WKBfuOD9oT/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -p /tmp/WKBfuOD9oT/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/WKBfuOD9oT/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -P /tmp/WKBfuOD9oT/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/WKBfuOD9oT/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -hm2 -M2 -q0.3 -Q0.7 /tmp/WKBfuOD9oT/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/WKBfuOD9oT/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Hu /tmp/WKBfuOD9oT/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -GVsnps /tmp/WKBfuOD9oT/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/WKBfuOD9oT/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -ne 'INDEL=1 || PV4[0]<0.006' /tmp/WKBfuOD9oT/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/WKBfuOD9oT/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -s ^NA00003 /tmp/WKBfuOD9oT/view.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/WKBfuOD9oT/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view /tmp/WKBfuOD9oT/view.omitgenotypes.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -asA /tmp/WKBfuOD9oT/view.vectors.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/WKBfuOD9oT/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -asB /tmp/WKBfuOD9oT/view.vectors.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/WKBfuOD9oT/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -H -i'FMT/FGS[0]="AAAAAA"' /tmp/WKBfuOD9oT/view.filter.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -H -i'FMT/FGS[2]="C"' /tmp/WKBfuOD9oT/view.filter.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -H -i'FMT/FGS[4]="EE"' /tmp/WKBfuOD9oT/view.filter.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -H -i'FMT/FRS[1]="BB"' /tmp/WKBfuOD9oT/view.filter.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -H -i'TXT0="text"' /tmp/WKBfuOD9oT/view.filter.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -T /<>/test/view.chrs.tab /tmp/WKBfuOD9oT/view.chrs.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/WKBfuOD9oT/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'TXT0="text"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'TXT0="text"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FRS[1]="BB"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FRS[1]="BB"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[0]="AAAAAA"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[0]="AAAAAA"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[1]="BBB"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[1]="BBB"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[4]="EE"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[4]="EE"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/STR="XX"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/STR="XX"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -H -C5:nonmajor /tmp/WKBfuOD9oT/view.minmaxac.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -H -c6:nonmajor /tmp/WKBfuOD9oT/view.minmaxac.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view -H -q0.3:major /tmp/WKBfuOD9oT/view.minmaxac.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call -mv /<>/test/mpileup.vcf | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call -Ob -mv /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call -mvg0 /<>/test/mpileup.vcf | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call -Ob -mvg0 /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call -mA -C alleles -T /tmp/WKBfuOD9oT/mpileup.tab.gz /<>/test/mpileup.vcf | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/WKBfuOD9oT/mpileup.tab.gz /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -mx -g2 -G2 /<>/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -mx -g2 -G2 /<>/test/filter.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<>/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<>/test/filter.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab /tmp/WKBfuOD9oT/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /<>/test/regions.tab /tmp/WKBfuOD9oT/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/WKBfuOD9oT/regions.tab.gz /tmp/WKBfuOD9oT/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/WKBfuOD9oT/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/WKBfuOD9oT/regions.tab.gz /tmp/WKBfuOD9oT/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/WKBfuOD9oT/regions.bed /tmp/WKBfuOD9oT/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/WKBfuOD9oT/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/WKBfuOD9oT/regions.bed /tmp/WKBfuOD9oT/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/WKBfuOD9oT/regions.bed.gz /tmp/WKBfuOD9oT/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/WKBfuOD9oT/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/WKBfuOD9oT/regions.bed.gz /tmp/WKBfuOD9oT/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/WKBfuOD9oT/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/WKBfuOD9oT/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/WKBfuOD9oT/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/WKBfuOD9oT/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/WKBfuOD9oT/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/WKBfuOD9oT/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/WKBfuOD9oT/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/WKBfuOD9oT/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/WKBfuOD9oT/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/WKBfuOD9oT/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ 2 sample(s) in common .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/WKBfuOD9oT/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/WKBfuOD9oT/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ 2 sample(s) in common .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/WKBfuOD9oT/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/WKBfuOD9oT/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/WKBfuOD9oT/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/WKBfuOD9oT/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<>/test/annotate3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<>/test/annotate3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x FORMAT /<>/test/annotate3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x FORMAT /<>/test/annotate3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/WKBfuOD9oT/annots4.vcf.gz -c +INFO /tmp/WKBfuOD9oT/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/WKBfuOD9oT/annots4.vcf.gz -c +INFO /tmp/WKBfuOD9oT/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/WKBfuOD9oT/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/WKBfuOD9oT/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat /tmp/WKBfuOD9oT/concat.1.a.vcf.gz /tmp/WKBfuOD9oT/concat.1.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/WKBfuOD9oT/concat.1.a.vcf.gz /tmp/WKBfuOD9oT/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat /tmp/WKBfuOD9oT/concat.1.a.bcf /tmp/WKBfuOD9oT/concat.1.b.bcf | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/WKBfuOD9oT/concat.1.a.bcf /tmp/WKBfuOD9oT/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -a /tmp/WKBfuOD9oT/concat.2.a.vcf.gz /tmp/WKBfuOD9oT/concat.2.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/WKBfuOD9oT/concat.2.a.vcf.gz /tmp/WKBfuOD9oT/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -a /tmp/WKBfuOD9oT/concat.2.a.bcf /tmp/WKBfuOD9oT/concat.2.b.bcf | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/WKBfuOD9oT/concat.2.a.bcf /tmp/WKBfuOD9oT/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -aD /tmp/WKBfuOD9oT/concat.2.a.vcf.gz /tmp/WKBfuOD9oT/concat.2.b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/WKBfuOD9oT/concat.2.a.vcf.gz /tmp/WKBfuOD9oT/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -aD /tmp/WKBfuOD9oT/concat.2.a.bcf /tmp/WKBfuOD9oT/concat.2.b.bcf | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/WKBfuOD9oT/concat.2.a.bcf /tmp/WKBfuOD9oT/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -l /tmp/WKBfuOD9oT/concat.3.a.vcf.gz /tmp/WKBfuOD9oT/concat.3.b.vcf.gz /tmp/WKBfuOD9oT/concat.3.0.vcf.gz /tmp/WKBfuOD9oT/concat.3.c.vcf.gz /tmp/WKBfuOD9oT/concat.3.d.vcf.gz /tmp/WKBfuOD9oT/concat.3.e.vcf.gz /tmp/WKBfuOD9oT/concat.3.f.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/WKBfuOD9oT/concat.3.a.vcf.gz /tmp/WKBfuOD9oT/concat.3.b.vcf.gz /tmp/WKBfuOD9oT/concat.3.0.vcf.gz /tmp/WKBfuOD9oT/concat.3.c.vcf.gz /tmp/WKBfuOD9oT/concat.3.d.vcf.gz /tmp/WKBfuOD9oT/concat.3.e.vcf.gz /tmp/WKBfuOD9oT/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -l /tmp/WKBfuOD9oT/concat.3.a.bcf /tmp/WKBfuOD9oT/concat.3.b.bcf /tmp/WKBfuOD9oT/concat.3.0.bcf /tmp/WKBfuOD9oT/concat.3.c.bcf /tmp/WKBfuOD9oT/concat.3.d.bcf /tmp/WKBfuOD9oT/concat.3.e.bcf /tmp/WKBfuOD9oT/concat.3.f.bcf | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/WKBfuOD9oT/concat.3.a.bcf /tmp/WKBfuOD9oT/concat.3.b.bcf /tmp/WKBfuOD9oT/concat.3.0.bcf /tmp/WKBfuOD9oT/concat.3.c.bcf /tmp/WKBfuOD9oT/concat.3.d.bcf /tmp/WKBfuOD9oT/concat.3.e.bcf /tmp/WKBfuOD9oT/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /<>/test/reheader.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/WKBfuOD9oT/reheader.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /tmp/WKBfuOD9oT/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/WKBfuOD9oT/reheader.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /tmp/WKBfuOD9oT/reheader.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /<>/test/reheader.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/WKBfuOD9oT/reheader.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /tmp/WKBfuOD9oT/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/WKBfuOD9oT/reheader.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /tmp/WKBfuOD9oT/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /<>/test/reheader.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/WKBfuOD9oT/reheader.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /tmp/WKBfuOD9oT/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/WKBfuOD9oT/reheader.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: cat /tmp/WKBfuOD9oT/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/WKBfuOD9oT/rename.map -Ov /tmp/WKBfuOD9oT/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/WKBfuOD9oT/rename.map -Ob /tmp/WKBfuOD9oT/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/WKBfuOD9oT/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/WKBfuOD9oT/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/WKBfuOD9oT/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: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/convert.vcf.gz | /<>/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: /<>/bcftools convert -g .,- /tmp/WKBfuOD9oT/convert.vcf.gz Sample file: - .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/convert.vcf.gz | /<>/bcftools convert -g .,- Sample file: - .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/WKBfuOD9oT/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: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/convert.vcf.gz | /<>/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: /<>/bcftools convert -g .,- --tag PL /tmp/WKBfuOD9oT/convert.vcf.gz Sample file: - .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL Sample file: - .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/WKBfuOD9oT/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: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/check.vcf.gz | /<>/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: /<>/bcftools convert -g .,- --vcf-ids /tmp/WKBfuOD9oT/check.vcf.gz Sample file: - .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids Sample file: - .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/WKBfuOD9oT/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: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/check.vcf.gz | /<>/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: /<>/bcftools convert -g .,- --chrom /tmp/WKBfuOD9oT/check.vcf.gz Sample file: - .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/check.vcf.gz | /<>/bcftools convert -g .,- --chrom Sample file: - .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/WKBfuOD9oT/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: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/check.vcf.gz | /<>/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: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/WKBfuOD9oT/check.vcf.gz Sample file: - .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids Sample file: - .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/WKBfuOD9oT/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: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/convert.vcf.gz | /<>/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: /<>/bcftools convert -h .,-,. /tmp/WKBfuOD9oT/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: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/convert.vcf.gz | /<>/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: /<>/bcftools convert -h .,.,- /tmp/WKBfuOD9oT/convert.vcf.gz Sample file: - .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/convert.vcf.gz | /<>/bcftools convert -h .,.,- Sample file: - .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/WKBfuOD9oT/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: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/convert.vcf.gz | /<>/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: /<>/bcftools convert --hapsample .,- /tmp/WKBfuOD9oT/convert.vcf.gz Sample file: - .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/convert.vcf.gz | /<>/bcftools convert --hapsample .,- Sample file: - .. ok test_vcf_convert_gvcf: /<>/bcftools convert --gvcf2vcf /tmp/WKBfuOD9oT/convert.gvcf.vcf.gz | grep -v ^##bcftools .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/WKBfuOD9oT/convert.gvcf.vcf.gz | /<>/bcftools convert --gvcf2vcf | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /<>/bcftools convert -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/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: /<>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.23andme | /<>/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: /<>/bcftools consensus /tmp/WKBfuOD9oT/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/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: /<>/bcftools consensus /tmp/WKBfuOD9oT/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/WKBfuOD9oT/consensus.1.chain.new > /dev/null; cat /tmp/WKBfuOD9oT/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/WKBfuOD9oT/consensus.1.chain.new: No such file or directory Non-zero status 1 .. failed ... test_vcf_consensus: /<>/bcftools consensus /tmp/WKBfuOD9oT/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/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: /<>/bcftools consensus /tmp/WKBfuOD9oT/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/WKBfuOD9oT/consensus.2.chain.new > /dev/null; cat /tmp/WKBfuOD9oT/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/WKBfuOD9oT/consensus.2.chain.new: No such file or directory Non-zero status 1 .. failed ... test_vcf_consensus: /<>/bcftools consensus /tmp/WKBfuOD9oT/consensus.vcf.gz -f /<>/test/consensus.fa -i -m /<>/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: /<>/bcftools consensus /tmp/WKBfuOD9oT/consensus.vcf.gz -f /<>/test/consensus.fa -i -m /<>/test/consensus.tab -c /tmp/WKBfuOD9oT/consensus.3.chain.new > /dev/null; cat /tmp/WKBfuOD9oT/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/WKBfuOD9oT/consensus.3.chain.new: No such file or directory Non-zero status 1 .. failed ... test_vcf_consensus: /<>/bcftools consensus /tmp/WKBfuOD9oT/consensus.vcf.gz -f /<>/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: /<>/bcftools consensus /tmp/WKBfuOD9oT/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/WKBfuOD9oT/consensus.4.chain.new > /dev/null; cat /tmp/WKBfuOD9oT/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/WKBfuOD9oT/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 '/<>' dh_auto_test: make -j4 test returned exit code 2 debian/rules:15: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 20170626-0726 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 7984 Build-Time: 25 Distribution: xenial-proposed Fail-Stage: build Host Architecture: armhf Install-Time: 20 Job: bcftools_1.2-2.dsc Machine Architecture: arm64 Package: bcftools Package-Time: 47 Source-Version: 1.2-2 Space: 7984 Status: attempted Version: 1.2-2 -------------------------------------------------------------------------------- Finished at 20170626-0726 Build needed 00:00:47, 7984k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8886985'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8886985/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8886985'] Unmounting chroot for build PACKAGEBUILD-8886985... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8886985'] Removing build PACKAGEBUILD-8886985