RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lcy01-13 4.4.0-87-generic #110-Ubuntu SMP Tue Jul 18 12:55:35 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_147 python-lpbuildd_147 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... 30 Jul 17:11:59 ntpdate[1758]: adjust time server 10.211.37.1 offset -0.000167 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-13171782', '/home/buildd/filecache-default/7fe38ae672de2c40a7e6ba74a0e6690544a5bb48'] Unpacking chroot for build PACKAGEBUILD-13171782 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-13171782'] Mounting chroot for build PACKAGEBUILD-13171782 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-13171782', 'deb http://ftpmaster.internal/ubuntu artful main universe', 'deb http://ftpmaster.internal/ubuntu artful-security main universe', 'deb http://ftpmaster.internal/ubuntu artful-updates main universe', 'deb http://ftpmaster.internal/ubuntu artful-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-13171782 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-13171782', 'i386'] Updating debian chroot for build PACKAGEBUILD-13171782 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main i386 Packages [1139 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [558 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe i386 Packages [8268 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4776 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main i386 Packages [124 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [60.5 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe i386 Packages [352 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [215 kB] Fetched 16.1 MB in 5s (2858 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.24 perl-modules-5.24 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: gcc-7-base libperl5.26 perl-modules-5.26 The following packages will be upgraded: advancecomp apt apt-transport-https base-files bash binutils bsdutils ca-certificates cpp cpp-6 debconf debianutils dmsetup dpkg dpkg-dev findutils g++ g++-6 gcc gcc-6 gcc-6-base grep init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcilkrts5 libdb5.3 libdevmapper1.02.1 libdpkg-perl libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libip4tc0 libitm1 libk5crypto3 libkmod2 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma5 libmount1 libmpx2 libnpth0 libp11-kit0 libpcre3 libperl5.24 libpng16-16 libpsl5 libquadmath0 libroken18-heimdal libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev login mount multiarch-support openssl passwd perl perl-base perl-modules-5.24 sensible-utils systemd systemd-sysv tar tzdata util-linux xz-utils 107 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 68.2 MB of archives. After this operation, 40.4 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main i386 debconf all 1.5.63 [136 kB] Get:2 http://ftpmaster.internal/ubuntu artful-proposed/main i386 perl i386 5.26.0-4 [205 kB] Get:3 http://ftpmaster.internal/ubuntu artful-proposed/main i386 perl-modules-5.26 all 5.26.0-4 [2762 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main i386 libperl5.24 i386 5.24.1-7ubuntu1 [3095 kB] Get:5 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libperl5.26 i386 5.26.0-4 [3149 kB] Get:6 http://ftpmaster.internal/ubuntu artful-proposed/main i386 perl-base i386 5.26.0-4 [1486 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main i386 perl-modules-5.24 all 5.24.1-7ubuntu1 [2664 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main i386 libc6-dev i386 2.24-12ubuntu1 [1870 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main i386 libc-dev-bin i386 2.24-12ubuntu1 [66.7 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main i386 linux-libc-dev i386 4.11.0-11.16 [932 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/main i386 gcc-7-base i386 7.1.0-10ubuntu1 [18.6 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libgcc1 i386 1:7.1.0-10ubuntu1 [47.0 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main i386 libc6 i386 2.24-12ubuntu1 [2278 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main i386 libdb5.3 i386 5.3.28-13 [733 kB] Get:15 http://ftpmaster.internal/ubuntu artful-proposed/main i386 init-system-helpers all 1.49 [37.0 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main i386 base-files i386 9.6ubuntu101 [59.1 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main i386 sensible-utils all 0.0.9+nmu1 [10.2 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main i386 debianutils i386 4.8.1.1 [85.7 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main i386 bash i386 4.4-5ubuntu1 [622 kB] Get:20 http://ftpmaster.internal/ubuntu artful-proposed/main i386 bsdutils i386 1:2.30.1-0ubuntu1 [61.9 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main i386 tar i386 1.29b-2 [252 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main i386 dpkg i386 1.18.24ubuntu1 [1164 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main i386 findutils i386 4.6.0+git+20170606-3 [303 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main i386 grep i386 3.1-2 [163 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main i386 login i386 1:4.2-3.2ubuntu2 [306 kB] Get:26 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libuuid1 i386 2.30.1-0ubuntu1 [15.5 kB] Get:27 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libblkid1 i386 2.30.1-0ubuntu1 [133 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main i386 libpcre3 i386 2:8.39-4 [227 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main i386 libselinux1 i386 2.6-3build1 [73.0 kB] Get:30 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libmount1 i386 2.30.1-0ubuntu1 [142 kB] Get:31 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libfdisk1 i386 2.30.1-0ubuntu1 [173 kB] Get:32 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libsmartcols1 i386 2.30.1-0ubuntu1 [85.1 kB] Get:33 http://ftpmaster.internal/ubuntu artful-proposed/main i386 util-linux i386 2.30.1-0ubuntu1 [974 kB] Get:34 http://ftpmaster.internal/ubuntu artful-proposed/main i386 mount i386 2.30.1-0ubuntu1 [136 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main i386 libc-bin i386 2.24-12ubuntu1 [591 kB] Get:36 http://ftpmaster.internal/ubuntu artful-proposed/main i386 liblzma5 i386 5.2.2-1.3 [98.5 kB] Get:37 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libstdc++6 i386 7.1.0-10ubuntu1 [436 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main i386 libapt-pkg5.0 i386 1.5~beta1 [860 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main i386 apt-transport-https i386 1.5~beta1 [38.6 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main i386 libp11-kit0 i386 0.23.7-3 [188 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main i386 libtasn1-6 i386 4.12-2.1 [38.7 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main i386 libgnutls30 i386 3.5.8-6ubuntu1 [692 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main i386 apt i386 1.5~beta1 [1138 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main i386 libip4tc0 i386 1.6.1-2ubuntu1 [20.5 kB] Get:45 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libapparmor1 i386 2.11.0-2ubuntu10 [31.2 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main i386 libaudit-common all 1:2.7.7-1ubuntu1 [4118 B] Get:47 http://ftpmaster.internal/ubuntu artful/main i386 libcap-ng0 i386 0.7.7-3build1 [11.1 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main i386 libaudit1 i386 1:2.7.7-1ubuntu1 [39.4 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main i386 libgpg-error0 i386 1.27-3 [39.4 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main i386 libgcrypt20 i386 1.7.8-2 [375 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main i386 libkmod2 i386 24-1ubuntu1 [46.0 kB] Get:52 http://ftpmaster.internal/ubuntu artful-proposed/main i386 systemd i386 234-2ubuntu1 [2885 kB] Get:53 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libsystemd0 i386 234-2ubuntu1 [232 kB] Get:54 http://ftpmaster.internal/ubuntu artful-proposed/main i386 init i386 1.49 [6038 B] Get:55 http://ftpmaster.internal/ubuntu artful-proposed/main i386 systemd-sysv i386 234-2ubuntu1 [13.8 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main i386 libsemanage-common all 2.6-2build1 [6738 B] Get:57 http://ftpmaster.internal/ubuntu artful/main i386 libsemanage1 i386 2.6-2build1 [89.9 kB] Get:58 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libudev1 i386 234-2ubuntu1 [59.5 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main i386 passwd i386 1:4.2-3.2ubuntu2 [790 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main i386 libdevmapper1.02.1 i386 2:1.02.137-2ubuntu2 [146 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main i386 dmsetup i386 2:1.02.137-2ubuntu2 [72.9 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main i386 libroken18-heimdal i386 7.4.0.dfsg.1-2 [44.5 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main i386 libasn1-8-heimdal i386 7.4.0.dfsg.1-2 [187 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main i386 libheimbase1-heimdal i386 7.4.0.dfsg.1-2 [32.0 kB] Get:65 http://ftpmaster.internal/ubuntu artful/main i386 libhcrypto4-heimdal i386 7.4.0.dfsg.1-2 [93.3 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main i386 libwind0-heimdal i386 7.4.0.dfsg.1-2 [49.1 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main i386 libhx509-5-heimdal i386 7.4.0.dfsg.1-2 [118 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main i386 libsqlite3-0 i386 3.19.3-3 [525 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main i386 libkrb5-26-heimdal i386 7.4.0.dfsg.1-2 [231 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main i386 libheimntlm0-heimdal i386 7.4.0.dfsg.1-2 [16.6 kB] Get:71 http://ftpmaster.internal/ubuntu artful/main i386 libgssapi3-heimdal i386 7.4.0.dfsg.1-2 [108 kB] Get:72 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libldap-2.4-2 i386 2.4.45+dfsg-1ubuntu1 [167 kB] Get:73 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libldap-common all 2.4.45+dfsg-1ubuntu1 [16.6 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main i386 libnpth0 i386 1.5-2 [7942 B] Get:75 http://ftpmaster.internal/ubuntu artful/main i386 libssl1.0.0 i386 1.0.2g-1ubuntu13 [910 kB] Get:76 http://ftpmaster.internal/ubuntu artful/main i386 multiarch-support i386 2.24-12ubuntu1 [6836 B] Get:77 http://ftpmaster.internal/ubuntu artful/main i386 tzdata all 2017b-2 [203 kB] Get:78 http://ftpmaster.internal/ubuntu artful-proposed/main i386 xz-utils i386 5.2.2-1.3 [88.6 kB] Get:79 http://ftpmaster.internal/ubuntu artful/main i386 openssl i386 1.0.2g-1ubuntu13 [506 kB] Get:80 http://ftpmaster.internal/ubuntu artful/main i386 ca-certificates all 20161130+nmu1 [186 kB] Get:81 http://ftpmaster.internal/ubuntu artful/main i386 libgssapi-krb5-2 i386 1.15.1-2 [129 kB] Get:82 http://ftpmaster.internal/ubuntu artful/main i386 libkrb5-3 i386 1.15.1-2 [300 kB] Get:83 http://ftpmaster.internal/ubuntu artful/main i386 libkrb5support0 i386 1.15.1-2 [34.0 kB] Get:84 http://ftpmaster.internal/ubuntu artful/main i386 libk5crypto3 i386 1.15.1-2 [88.3 kB] Get:85 http://ftpmaster.internal/ubuntu artful/main i386 libidn2-0 i386 2.0.2-1 [92.8 kB] Get:86 http://ftpmaster.internal/ubuntu artful/main i386 libpng16-16 i386 1.6.30-2 [181 kB] Get:87 http://ftpmaster.internal/ubuntu artful/main i386 libpsl5 i386 0.17.0-5 [41.3 kB] Get:88 http://ftpmaster.internal/ubuntu artful/main i386 advancecomp i386 2.0-1 [206 kB] Get:89 http://ftpmaster.internal/ubuntu artful-proposed/main i386 binutils i386 2.29-1ubuntu1 [2689 kB] Get:90 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libquadmath0 i386 7.1.0-10ubuntu1 [205 kB] Get:91 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libitm1 i386 7.1.0-10ubuntu1 [30.3 kB] Get:92 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libmpx2 i386 7.1.0-10ubuntu1 [13.0 kB] Get:93 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libubsan0 i386 7.1.0-10ubuntu1 [134 kB] Get:94 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libcilkrts5 i386 7.1.0-10ubuntu1 [47.4 kB] Get:95 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libgomp1 i386 7.1.0-10ubuntu1 [80.3 kB] Get:96 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libatomic1 i386 7.1.0-10ubuntu1 [9704 B] Get:97 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libasan3 i386 6.4.0-2ubuntu1 [308 kB] Get:98 http://ftpmaster.internal/ubuntu artful-proposed/main i386 g++-6 i386 6.4.0-2ubuntu1 [7642 kB] Get:99 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libstdc++-6-dev i386 6.4.0-2ubuntu1 [1456 kB] Get:100 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Get:110 http://ftpmaster.internal/ubuntu artful/main i386 libusb-0.1-4 i386 2:0.1.12-31 [17.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 68.2 MB in 6s (10.4 MB/s) (Reading database ... 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(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 ... 14308 files and directories currently installed.) Preparing to unpack .../apt_1.5~beta1_i386.deb ... Unpacking apt (1.5~beta1) over (1.4.1ubuntu2) ... Setting up apt (1.5~beta1) ... (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 ... 14307 files and directories currently installed.) Preparing to unpack .../libip4tc0_1.6.1-2ubuntu1_i386.deb ... Unpacking libip4tc0:i386 (1.6.1-2ubuntu1) over (1.6.0-3ubuntu2) ... Preparing to unpack .../libapparmor1_2.11.0-2ubuntu10_i386.deb ... Unpacking libapparmor1:i386 (2.11.0-2ubuntu10) over (2.11.0-2ubuntu4) ... Preparing to unpack .../libaudit-common_1%3a2.7.7-1ubuntu1_all.deb ... Unpacking libaudit-common (1:2.7.7-1ubuntu1) over (1:2.6.6-1ubuntu1) ... Setting up libaudit-common (1:2.7.7-1ubuntu1) ... (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 ... 14307 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.7.7-3build1_i386.deb ... Unpacking libcap-ng0:i386 (0.7.7-3build1) over (0.7.7-3) ... Setting up libcap-ng0:i386 (0.7.7-3build1) ... (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 ... 14307 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a2.7.7-1ubuntu1_i386.deb ... Unpacking libaudit1:i386 (1:2.7.7-1ubuntu1) over (1:2.6.6-1ubuntu1) ... Setting up libaudit1:i386 (1:2.7.7-1ubuntu1) ... (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 ... 14307 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.27-3_i386.deb ... Unpacking libgpg-error0:i386 (1.27-3) over (1.26-2) ... Setting up libgpg-error0:i386 (1.27-3) ... (Reading database ... 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(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 ... 14307 files and directories currently installed.) Preparing to unpack .../libkmod2_24-1ubuntu1_i386.deb ... Unpacking libkmod2:i386 (24-1ubuntu1) over (22-1.1ubuntu1) ... Preparing to unpack .../systemd_234-2ubuntu1_i386.deb ... Unpacking systemd (234-2ubuntu1) over (232-21ubuntu3) ... dpkg: warning: unable to delete old directory '/etc/dbus-1/system.d': Directory not empty dpkg: warning: unable to delete old directory '/etc/dbus-1': Directory not empty Preparing to unpack .../libsystemd0_234-2ubuntu1_i386.deb ... Unpacking libsystemd0:i386 (234-2ubuntu1) over (232-21ubuntu3) ... Setting up libsystemd0:i386 (234-2ubuntu1) ... (Reading database ... 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Installing new version of config file /etc/systemd/resolved.conf ... Created symlink /etc/systemd/system/dbus-org.freedesktop.resolve1.service -> /lib/systemd/system/systemd-resolved.service. Created symlink /etc/systemd/system/multi-user.target.wants/systemd-resolved.service -> /lib/systemd/system/systemd-resolved.service. addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.hostname1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.locale1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.login1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.network1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.resolve1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.systemd1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.timedate1.conf ... 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Unpacking cpp (4:6.3.0-2ubuntu2) over (4:6.3.0-2ubuntu1) ... Preparing to unpack .../46-dpkg-dev_1.18.24ubuntu1_all.deb ... Unpacking dpkg-dev (1.18.24ubuntu1) over (1.18.23ubuntu4) ... Preparing to unpack .../47-libdpkg-perl_1.18.24ubuntu1_all.deb ... Unpacking libdpkg-perl (1.18.24ubuntu1) over (1.18.23ubuntu4) ... Preparing to unpack .../48-gcc_4%3a6.3.0-2ubuntu2_i386.deb ... Removing old gcc doc directory. Unpacking gcc (4:6.3.0-2ubuntu2) over (4:6.3.0-2ubuntu1) ... Preparing to unpack .../49-g++_4%3a6.3.0-2ubuntu2_i386.deb ... Unpacking g++ (4:6.3.0-2ubuntu2) over (4:6.3.0-2ubuntu1) ... Preparing to unpack .../50-libusb-0.1-4_2%3a0.1.12-31_i386.deb ... Unpacking libusb-0.1-4:i386 (2:0.1.12-31) over (2:0.1.12-30) ... Setting up libquadmath0:i386 (7.1.0-10ubuntu1) ... Setting up libnpth0:i386 (1.5-2) ... Setting up libgomp1:i386 (7.1.0-10ubuntu1) ... Setting up libatomic1:i386 (7.1.0-10ubuntu1) ... Setting up perl-modules-5.24 (5.24.1-7ubuntu1) ... Setting up libperl5.24:i386 (5.24.1-7ubuntu1) ... Setting up libcc1-0:i386 (7.1.0-10ubuntu1) ... Setting up apt-transport-https (1.5~beta1) ... Setting up libidn2-0:i386 (2.0.2-1) ... Setting up libssl1.0.0:i386 (1.0.2g-1ubuntu13) ... Setting up libpng16-16:i386 (1.6.30-2) ... Setting up libldap-common (2.4.45+dfsg-1ubuntu1) ... Setting up libcilkrts5:i386 (7.1.0-10ubuntu1) ... Setting up libpsl5:i386 (0.17.0-5) ... Setting up multiarch-support (2.24-12ubuntu1) ... Setting up tzdata (2017b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Jul 30 17:12:49 UTC 2017. Universal Time is now: Sun Jul 30 17:12:49 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (234-2ubuntu1) ... Setting up libubsan0:i386 (7.1.0-10ubuntu1) ... Setting up gcc-6-base:i386 (6.4.0-2ubuntu1) ... Setting up linux-libc-dev:i386 (4.11.0-11.16) ... Setting up advancecomp (2.0-1) ... Setting up libroken18-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up libdevmapper1.02.1:i386 (2:1.02.137-2ubuntu2) ... Setting up perl-modules-5.26 (5.26.0-4) ... Setting up libkrb5support0:i386 (1.15.1-2) ... Setting up libmpx2:i386 (7.1.0-10ubuntu1) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Setting up libperl5.26:i386 (5.26.0-4) ... Setting up xz-utils (5.2.2-1.3) ... Setting up libheimbase1-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up openssl (1.0.2g-1ubuntu13) ... Setting up libsqlite3-0:i386 (3.19.3-3) ... Setting up dmsetup (2:1.02.137-2ubuntu2) ... Setting up binutils (2.29-1ubuntu1) ... Setting up cpp-6 (6.4.0-2ubuntu1) ... Setting up libc-dev-bin (2.24-12ubuntu1) ... Setting up ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 7 removed; done. Setting up libc6-dev:i386 (2.24-12ubuntu1) ... Setting up libusb-0.1-4:i386 (2:0.1.12-31) ... Setting up libitm1:i386 (7.1.0-10ubuntu1) ... Setting up cpp (4:6.3.0-2ubuntu2) ... Setting up libk5crypto3:i386 (1.15.1-2) ... Setting up libasan3:i386 (6.4.0-2ubuntu1) ... Setting up libgcc-6-dev:i386 (6.4.0-2ubuntu1) ... Setting up libstdc++-6-dev:i386 (6.4.0-2ubuntu1) ... Setting up libwind0-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up init (1.49) ... Setting up libasn1-8-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up libhcrypto4-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up libhx509-5-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up gcc-6 (6.4.0-2ubuntu1) ... Setting up g++-6 (6.4.0-2ubuntu1) ... Setting up perl (5.26.0-4) ... Removing obsolete conffile /etc/perl/sitecustomize.pl ... Setting up libkrb5-3:i386 (1.15.1-2) ... Setting up libkrb5-26-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up libheimntlm0-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up libdpkg-perl (1.18.24ubuntu1) ... Setting up gcc (4:6.3.0-2ubuntu2) ... Setting up libgssapi-krb5-2:i386 (1.15.1-2) ... Setting up dpkg-dev (1.18.24ubuntu1) ... Setting up g++ (4:6.3.0-2ubuntu2) ... Setting up libgssapi3-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up libldap-2.4-2:i386 (2.4.45+dfsg-1ubuntu1) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Processing triggers for ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-13171782', 'i386', 'artful-proposed', '-c', 'chroot:autobuild', '--arch=i386', '--dist=artful-proposed', '--purge=never', '--nolog', 'bcftools_1.4.1-3.dsc'] Initiating build PACKAGEBUILD-13171782 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-87-generic #110-Ubuntu SMP Tue Jul 18 12:55:35 UTC 2017 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-13.buildd +==============================================================================+ | bcftools 1.4.1-3 (i386) 30 Jul 2017 17:13 | +==============================================================================+ Package: bcftools Version: 1.4.1-3 Source Version: 1.4.1-3 Distribution: artful-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/bcftools-oc6NtZ/bcftools-1.4.1' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-oc6NtZ' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13171782/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bcftools_1.4.1-3.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-Q_oaTE/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-Q_oaTE/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Q_oaTE/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Q_oaTE/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Q_oaTE/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-Q_oaTE/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (210 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 packages were automatically installed and are no longer required: libperl5.24 perl-modules-5.24 Use 'sudo apt autoremove' to remove them. 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 780 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Q_oaTE/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [780 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 780 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 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Merged Build-Depends: debhelper (>= 10), zlib1g-dev, libhts-dev (>= 1.3.1), libgsl-dev, tabix, libio-pty-perl Filtered Build-Depends: debhelper (>= 10), zlib1g-dev, libhts-dev (>= 1.3.1), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<>/resolver-zgiT2B/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. Ign:1 copy:/<>/resolver-zgiT2B/apt_archive ./ InRelease Get:2 copy:/<>/resolver-zgiT2B/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-zgiT2B/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-zgiT2B/apt_archive ./ Sources [247 B] Get:5 copy:/<>/resolver-zgiT2B/apt_archive ./ Packages [564 B] Fetched 2930 B in 0s (245 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 packages were automatically installed and are no longer required: libperl5.24 perl-modules-5.24 Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl2 libhts-dev libhts2 libicu57 libio-pty-perl libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl2 libhts-dev libhts2 libicu57 libio-pty-perl libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 37 newly installed, 1 to remove and 0 not upgraded. Need to get 19.7 MB of archives. After this operation, 75.4 MB of additional disk space will be used. Get:1 copy:/<>/resolver-zgiT2B/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [818 B] Get:2 http://ftpmaster.internal/ubuntu artful/main i386 groff-base i386 1.22.3-9 [1163 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main i386 libbsd0 i386 0.8.6-1 [45.1 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main i386 bsdmainutils i386 9.0.12+nmu1ubuntu1 [181 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main i386 libpipeline1 i386 1.4.2-1 [26.8 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main i386 man-db i386 2.7.6.1-2 [906 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main i386 libmagic-mgc i386 1:5.30-1 [181 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main i386 libmagic1 i386 1:5.30-1 [74.3 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main i386 file i386 1:5.30-1 [21.7 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main i386 gettext-base i386 0.19.8.1-2ubuntu1 [48.9 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main i386 libglib2.0-0 i386 2.53.4-1 [1229 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main i386 libicu57 i386 57.1-6 [7837 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main i386 libxml2 i386 2.9.4+dfsg1-3build1 [691 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main i386 libsigsegv2 i386 2.11-1 [13.5 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main i386 m4 i386 1.4.18-1 [196 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main i386 autoconf all 2.69-10 [321 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main i386 autotools-dev all 20161112.1 [39.5 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main i386 automake all 1:1.15-6ubuntu1 [509 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main i386 autopoint all 0.19.8.1-2ubuntu1 [411 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main i386 libtool all 2.4.6-2 [194 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main i386 dh-autoreconf all 14 [15.5 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main i386 libarchive-zip-perl all 1.59-1 [84.0 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main i386 libfile-stripnondeterminism-perl all 0.038-1 [13.3 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main i386 libtimedate-perl all 2.3000-2 [37.5 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main i386 dh-strip-nondeterminism all 0.038-1 [5026 B] Get:26 http://ftpmaster.internal/ubuntu artful/main i386 libcroco3 i386 0.6.12-1 [87.5 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main i386 gettext i386 0.19.8.1-2ubuntu1 [1088 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main i386 po-debconf all 1.0.20 [232 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main i386 debhelper all 10.6.4ubuntu1 [875 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main i386 libgsl2 i386 2.4+dfsg-2 [873 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main i386 libgsl-dev i386 2.4+dfsg-2 [1035 kB] Get:33 http://ftpmaster.internal/ubuntu artful/universe i386 libhts2 i386 1.4.1-5 [306 kB] Get:34 http://ftpmaster.internal/ubuntu artful/universe i386 libhts-dev i386 1.4.1-5 [412 kB] Get:35 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libio-pty-perl i386 1:1.08-1.1build4 [30.8 kB] Get:36 http://ftpmaster.internal/ubuntu artful/universe i386 tabix i386 1.4.1-5 [338 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main i386 zlib1g-dev i386 1:1.2.11.dfsg-0ubuntu1 [171 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.7 MB in 1s (19.1 MB/s) (Reading database ... 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Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up libgsl-dev (2.4+dfsg-2) ... Setting up libhts-dev:i386 (1.4.1-5) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.038-1) ... Setting up debhelper (10.6.4ubuntu1) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... (Reading database ... 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Processing triggers for libc-bin (2.24-12ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-87-generic amd64 (i686) Toolchain package versions: binutils_2.29-1ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.4.0-2ubuntu1 gcc-6_6.4.0-2ubuntu1 libc6-dev_2.24-12ubuntu1 libstdc++-6-dev_6.4.0-2ubuntu1 libstdc++6_7.1.0-10ubuntu1 linux-libc-dev_4.11.0-11.16 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.5~beta1 apt-transport-https_1.5~beta1 autoconf_2.69-10 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu101 base-passwd_3.5.43 bash_4.4-5ubuntu1 binutils_2.29-1ubuntu1 bsdmainutils_9.0.12+nmu1ubuntu1 bsdutils_1:2.30.1-0ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu2 cpp-6_6.4.0-2ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.63 debhelper_10.6.4ubuntu1 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2ubuntu2 dpkg_1.18.24ubuntu1 dpkg-dev_1.18.24ubuntu1 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-1ubuntu2 file_1:5.30-1 findutils_4.6.0+git+20170606-3 g++_4:6.3.0-2ubuntu2 g++-6_6.4.0-2ubuntu1 gcc_4:6.3.0-2ubuntu2 gcc-6_6.4.0-2ubuntu1 gcc-6-base_6.4.0-2ubuntu1 gcc-7-base_7.1.0-10ubuntu1 gettext_0.19.8.1-2ubuntu1 gettext-base_0.19.8.1-2ubuntu1 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 gpgv_2.1.15-1ubuntu7 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.49 init-system-helpers_1.49 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu10 libapt-pkg5.0_1.5~beta1 libarchive-zip-perl_1.59-1 libasan3_6.4.0-2ubuntu1 libasn1-8-heimdal_7.4.0.dfsg.1-2 libassuan0_2.4.3-2 libatomic1_7.1.0-10ubuntu1 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libhcrypto4-heimdal_7.4.0.dfsg.1-2 libheimbase1-heimdal_7.4.0.dfsg.1-2 libheimntlm0-heimdal_7.4.0.dfsg.1-2 libhogweed4_3.3-1 libhts-dev_1.4.1-5 libhts2_1.4.1-5 libhx509-5-heimdal_7.4.0.dfsg.1-2 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libio-pty-perl_1:1.08-1.1build4 libip4tc0_1.6.1-2ubuntu1 libisl15_0.18-1 libitm1_7.1.0-10ubuntu1 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_24-1ubuntu1 libkrb5-26-heimdal_7.4.0.dfsg.1-2 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1ubuntu1 libldap-common_2.4.45+dfsg-1ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.30.1-0ubuntu1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libmpx2_7.1.0-10ubuntu1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 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tzdata_2017b-2 ubuntu-keyring_2016.10.27 util-linux_2.30.1-0ubuntu1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu1 zlib1g-dev_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Jul 29 08:57:28 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.4.1-3.dsc dpkg-source: info: extracting bcftools in bcftools-1.4.1 dpkg-source: info: unpacking bcftools_1.4.1.orig.tar.gz dpkg-source: info: unpacking bcftools_1.4.1-3.debian.tar.xz dpkg-source: info: applying external-libs.patch dpkg-source: info: applying compiler-flags.patch dpkg-source: info: applying destdir.patch dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying test-regidx-unsigned-char.patch dpkg-source: info: applying fix-bufffer-overflow.patch dpkg-source: info: applying fix-test_vcf_query.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=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: info: source package bcftools dpkg-buildpackage: info: source version 1.4.1-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build bcftools-1.4.1 dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --parallel dh_testdir dh_auto_clean make -j4 distclean make[1]: Entering directory '/<>' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f gmon.out *.o *~ bcftools version.h plugins/*.so plugins/*.P rm -rf *.dSYM plugins/*.dSYM test/*.dSYM rm -f TAGS make[1]: Leaving directory '/<>' dh_autoreconf_clean dh_clean debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel dh_update_autotools_config -a -O--parallel dh_autoreconf -a -O--parallel dh_auto_configure -a -O--parallel dh_auto_build -a -O--parallel make -j4 make[1]: Entering directory '/<>' echo '#define BCFTOOLS_VERSION "1.4.1"' > version.h cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfplugin.o vcfplugin.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polysomy.o polysomy.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o peakfit.o peakfit.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixploidy.so ploidy.c version.c plugins/fixploidy.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/isecGT.so version.c plugins/isecGT.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c cc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lm -lz -ldl -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lm -lz -ldl -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o ccall.o em.o prob1.o kmin.o polysomy.o peakfit.o -lpthread -lgsl -lgslcblas -lm -lz -ldl -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts make[1]: Leaving directory '/<>' dh_auto_test -a -O--parallel make -j4 test make[1]: Entering directory '/<>' ./test/test-regidx ./test/test.pl --exec bgzip=/usr/bin/bgzip --exec tabix=/usr/bin/tabix test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools polysomy .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: /usr/bin/tabix /tmp/tISchhPFtJ/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/tISchhPFtJ/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: /usr/bin/tabix /tmp/tISchhPFtJ/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/tISchhPFtJ/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/tISchhPFtJ/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/tISchhPFtJ/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/tISchhPFtJ/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/tISchhPFtJ/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/tISchhPFtJ/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/tISchhPFtJ/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/tISchhPFtJ/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/tISchhPFtJ/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/tISchhPFtJ/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/tISchhPFtJ/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/tISchhPFtJ/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/tISchhPFtJ/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/tISchhPFtJ/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tISchhPFtJ/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tISchhPFtJ/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tISchhPFtJ/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/tISchhPFtJ/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/tISchhPFtJ/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/tISchhPFtJ/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tISchhPFtJ/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tISchhPFtJ/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tISchhPFtJ/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/tISchhPFtJ/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/tISchhPFtJ/check.vcf.gz | /<>/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /<>/misc/plot-vcfstats -m /tmp/tISchhPFtJ/check.1.chk /tmp/tISchhPFtJ/check.2.chk /tmp/tISchhPFtJ/check.3.chk /tmp/tISchhPFtJ/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/tISchhPFtJ/stats.a.vcf.gz /tmp/tISchhPFtJ/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/tISchhPFtJ/stats.a.vcf.gz /tmp/tISchhPFtJ/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/tISchhPFtJ/isec.a.vcf.gz /tmp/tISchhPFtJ/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/tISchhPFtJ/isec.a.vcf.gz /tmp/tISchhPFtJ/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/tISchhPFtJ/isec.a.vcf.gz /tmp/tISchhPFtJ/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/tISchhPFtJ/isec.a.vcf.gz /tmp/tISchhPFtJ/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/tISchhPFtJ/isec.a.vcf.gz /tmp/tISchhPFtJ/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/tISchhPFtJ/isec.a.vcf.gz /tmp/tISchhPFtJ/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/tISchhPFtJ/isec.a.vcf.gz /tmp/tISchhPFtJ/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/tISchhPFtJ/isec.a.vcf.gz /tmp/tISchhPFtJ/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/tISchhPFtJ/isec.a.vcf.gz /tmp/tISchhPFtJ/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/tISchhPFtJ/isec.a.vcf.gz /tmp/tISchhPFtJ/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/tISchhPFtJ/isec.tab.gz /tmp/tISchhPFtJ/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/tISchhPFtJ/isec.tab.gz /tmp/tISchhPFtJ/isec.a.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/tISchhPFtJ/merge.a.vcf.gz /tmp/tISchhPFtJ/merge.b.vcf.gz /tmp/tISchhPFtJ/merge.c.vcf.gz The outputs differ: /<>/test/merge.abc.out /<>/test/merge.abc.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/tISchhPFtJ/merge.a.vcf.gz /tmp/tISchhPFtJ/merge.b.vcf.gz /tmp/tISchhPFtJ/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.abc.out /<>/test/merge.abc.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/tISchhPFtJ/merge.a.vcf.gz /tmp/tISchhPFtJ/merge.b.vcf.gz /tmp/tISchhPFtJ/merge.c.vcf.gz The outputs differ: /<>/test/merge.abc.2.out /<>/test/merge.abc.2.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -Fx /tmp/tISchhPFtJ/merge.a.vcf.gz /tmp/tISchhPFtJ/merge.b.vcf.gz /tmp/tISchhPFtJ/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.abc.2.out /<>/test/merge.abc.2.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/tISchhPFtJ/merge.a.vcf.gz /tmp/tISchhPFtJ/merge.b.vcf.gz /tmp/tISchhPFtJ/merge.c.vcf.gz The outputs differ: /<>/test/merge.abc.3.out /<>/test/merge.abc.3.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -0 /tmp/tISchhPFtJ/merge.a.vcf.gz /tmp/tISchhPFtJ/merge.b.vcf.gz /tmp/tISchhPFtJ/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.abc.3.out /<>/test/merge.abc.3.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/tISchhPFtJ/merge.2.a.vcf.gz /tmp/tISchhPFtJ/merge.2.b.vcf.gz The outputs differ: /<>/test/merge.2.none.out /<>/test/merge.2.none.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m none /tmp/tISchhPFtJ/merge.2.a.vcf.gz /tmp/tISchhPFtJ/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.2.none.out /<>/test/merge.2.none.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/tISchhPFtJ/merge.2.a.vcf.gz /tmp/tISchhPFtJ/merge.2.b.vcf.gz The outputs differ: /<>/test/merge.2.both.out /<>/test/merge.2.both.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m both /tmp/tISchhPFtJ/merge.2.a.vcf.gz /tmp/tISchhPFtJ/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.2.both.out /<>/test/merge.2.both.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/tISchhPFtJ/merge.2.a.vcf.gz /tmp/tISchhPFtJ/merge.2.b.vcf.gz The outputs differ: /<>/test/merge.2.all.out /<>/test/merge.2.all.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m all /tmp/tISchhPFtJ/merge.2.a.vcf.gz /tmp/tISchhPFtJ/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.2.all.out /<>/test/merge.2.all.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/tISchhPFtJ/merge.3.a.vcf.gz /tmp/tISchhPFtJ/merge.3.b.vcf.gz The outputs differ: /<>/test/merge.3.out /<>/test/merge.3.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/tISchhPFtJ/merge.3.a.vcf.gz /tmp/tISchhPFtJ/merge.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.3.out /<>/test/merge.3.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/tISchhPFtJ/merge.4.a.vcf.gz /tmp/tISchhPFtJ/merge.4.b.vcf.gz The outputs differ: /<>/test/merge.4.out /<>/test/merge.4.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m id /tmp/tISchhPFtJ/merge.4.a.vcf.gz /tmp/tISchhPFtJ/merge.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.4.out /<>/test/merge.4.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/tISchhPFtJ/gvcf.merge.1.vcf.gz /tmp/tISchhPFtJ/gvcf.merge.2.vcf.gz /tmp/tISchhPFtJ/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/tISchhPFtJ/gvcf.merge.1.vcf.gz /tmp/tISchhPFtJ/gvcf.merge.2.vcf.gz /tmp/tISchhPFtJ/gvcf.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/tISchhPFtJ/merge.gvcf.2.a.vcf.gz /tmp/tISchhPFtJ/merge.gvcf.2.b.vcf.gz /tmp/tISchhPFtJ/merge.gvcf.2.c.vcf.gz The outputs differ: /<>/test/merge.gvcf.2.out /<>/test/merge.gvcf.2.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/tISchhPFtJ/merge.gvcf.2.a.vcf.gz /tmp/tISchhPFtJ/merge.gvcf.2.b.vcf.gz /tmp/tISchhPFtJ/merge.gvcf.2.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.gvcf.2.out /<>/test/merge.gvcf.2.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version /tmp/tISchhPFtJ/merge.5.a.vcf.gz /tmp/tISchhPFtJ/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/tISchhPFtJ/merge.5.a.vcf.gz /tmp/tISchhPFtJ/merge.5.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/tISchhPFtJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/query.2.vcf.gz | /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/tISchhPFtJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/tISchhPFtJ/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/tISchhPFtJ/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/tISchhPFtJ/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/tISchhPFtJ/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/tISchhPFtJ/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/filter-missing-floats.vcf.gz | /<>/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/tISchhPFtJ/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/filter-missing-floats.vcf.gz | /<>/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /<>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/tISchhPFtJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/missing.vcf.gz | /<>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /<>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/tISchhPFtJ/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tISchhPFtJ/query.filter.2.vcf.gz | /<>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx -f /<>/test/norm.fa /tmp/tISchhPFtJ/norm.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -cx -f /<>/test/norm.fa /tmp/tISchhPFtJ/norm.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/tISchhPFtJ/norm.split.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.split.out /<>/test/norm.split.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/tISchhPFtJ/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.split.out /<>/test/norm.split.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/tISchhPFtJ/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/tISchhPFtJ/norm.split.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- -f /<>/test/norm.fa /tmp/tISchhPFtJ/norm.split.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.split.and.norm.out /<>/test/norm.split.and.norm.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m- -f /<>/test/norm.fa /tmp/tISchhPFtJ/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.split.and.norm.out /<>/test/norm.split.and.norm.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/tISchhPFtJ/norm.merge.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.merge.out /<>/test/norm.merge.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/tISchhPFtJ/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.merge.out /<>/test/norm.merge.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/tISchhPFtJ/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/tISchhPFtJ/norm.merge.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/tISchhPFtJ/norm.merge.3.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.merge.3.out /<>/test/norm.merge.3.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/tISchhPFtJ/norm.merge.3.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.merge.3.out /<>/test/norm.merge.3.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/tISchhPFtJ/norm.merge.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.merge.strict.out /<>/test/norm.merge.strict.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ -s /tmp/tISchhPFtJ/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.merge.strict.out /<>/test/norm.merge.strict.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -Nc s -f /<>/test/norm.fa /tmp/tISchhPFtJ/norm.setref.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/tISchhPFtJ/norm.setref.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.fa /tmp/tISchhPFtJ/norm.telomere.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/tISchhPFtJ/norm.telomere.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/tISchhPFtJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/tISchhPFtJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/tISchhPFtJ/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/tISchhPFtJ/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/tISchhPFtJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/tISchhPFtJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/tISchhPFtJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/tISchhPFtJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/tISchhPFtJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/tISchhPFtJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/tISchhPFtJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/tISchhPFtJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/tISchhPFtJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/tISchhPFtJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/tISchhPFtJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/tISchhPFtJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/tISchhPFtJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/tISchhPFtJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/tISchhPFtJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/tISchhPFtJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/tISchhPFtJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/tISchhPFtJ/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/tISchhPFtJ/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/tISchhPFtJ/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/tISchhPFtJ/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/tISchhPFtJ/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/tISchhPFtJ/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/tISchhPFtJ/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/tISchhPFtJ/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/tISchhPFtJ/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/tISchhPFtJ/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/tISchhPFtJ/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/tISchhPFtJ/view.vectors.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/tISchhPFtJ/view.vectors.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[0]="AAAAAA"' /tmp/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[2]="C"' /tmp/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[4]="EE"' /tmp/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[1]="BB"' /tmp/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/tISchhPFtJ/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/tISchhPFtJ/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/tISchhPFtJ/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/tISchhPFtJ/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/tISchhPFtJ/filter.2.vcf.gz 1:3062917-3157410 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'TXT0="text"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'TXT0="text"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FRS[1]="BB"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FRS[1]="BB"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[0]="AAAAAA"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[0]="AAAAAA"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[1]="BBB"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[1]="BBB"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[4]="EE"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[4]="EE"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/STR="XX"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/STR="XX"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -C5:nonmajor /tmp/tISchhPFtJ/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/tISchhPFtJ/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/tISchhPFtJ/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/tISchhPFtJ/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/tISchhPFtJ/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/tISchhPFtJ/view.filter.annovar.vcf.gz .. ok test_vcf_call: /<>/bcftools call --no-version -mv /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv /<>/test/mpileup.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mg0 /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mg0 /<>/test/mpileup.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/tISchhPFtJ/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/tISchhPFtJ/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv /<>/test/mpileup.c.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv /<>/test/mpileup.c.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.c.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.c.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.c.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -mx -g2 -G2 /<>/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -mx -g2 -G2 /<>/test/filter.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<>/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<>/test/filter.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'ALT="."' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'ALT="."' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -S . -i 'FORMAT/TEST3<25' /<>/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /<>/test/filter.4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -i 'FORMAT/TEST4<25' /<>/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /<>/test/filter.4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab /tmp/tISchhPFtJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/tISchhPFtJ/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/tISchhPFtJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/tISchhPFtJ/regions.tab.gz /tmp/tISchhPFtJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/tISchhPFtJ/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/tISchhPFtJ/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/tISchhPFtJ/regions.tab.gz /tmp/tISchhPFtJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/tISchhPFtJ/regions.bed /tmp/tISchhPFtJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/tISchhPFtJ/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/tISchhPFtJ/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/tISchhPFtJ/regions.bed /tmp/tISchhPFtJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/tISchhPFtJ/regions.bed.gz /tmp/tISchhPFtJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/tISchhPFtJ/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/tISchhPFtJ/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/tISchhPFtJ/regions.bed.gz /tmp/tISchhPFtJ/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/tISchhPFtJ/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/tISchhPFtJ/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/tISchhPFtJ/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate4.out /<>/test/annotate4.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/tISchhPFtJ/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate4.out /<>/test/annotate4.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/tISchhPFtJ/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/tISchhPFtJ/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x FORMAT /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x FORMAT /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annots4.vcf.gz -c +INFO /tmp/tISchhPFtJ/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate8.out /<>/test/annotate8.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annots4.vcf.gz -c +INFO /tmp/tISchhPFtJ/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate8.out /<>/test/annotate8.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate8.out /<>/test/annotate8.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate8.out /<>/test/annotate8.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annots10.tab.gz -h /<>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<>/test/annotate10.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate10.out /<>/test/annotate10.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annots10.tab.gz -h /<>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<>/test/annotate10.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate10.out /<>/test/annotate10.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/tISchhPFtJ/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate11.out /<>/test/annotate11.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/tISchhPFtJ/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate11.out /<>/test/annotate11.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<>/test/annotate2.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate11.out /<>/test/annotate11.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<>/test/annotate2.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate11.out /<>/test/annotate11.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/tISchhPFtJ/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/tISchhPFtJ/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/tISchhPFtJ/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/tISchhPFtJ/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tISchhPFtJ/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tISchhPFtJ/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/tISchhPFtJ/concat.1.a.vcf.gz /tmp/tISchhPFtJ/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/tISchhPFtJ/concat.1.a.vcf.gz /tmp/tISchhPFtJ/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/tISchhPFtJ/concat.1.a.bcf /tmp/tISchhPFtJ/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/tISchhPFtJ/concat.1.a.bcf /tmp/tISchhPFtJ/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/tISchhPFtJ/concat.2.a.vcf.gz /tmp/tISchhPFtJ/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/tISchhPFtJ/concat.2.a.vcf.gz /tmp/tISchhPFtJ/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/tISchhPFtJ/concat.2.a.bcf /tmp/tISchhPFtJ/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/tISchhPFtJ/concat.2.a.bcf /tmp/tISchhPFtJ/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/tISchhPFtJ/concat.2.a.vcf.gz /tmp/tISchhPFtJ/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/tISchhPFtJ/concat.2.a.vcf.gz /tmp/tISchhPFtJ/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/tISchhPFtJ/concat.2.a.bcf /tmp/tISchhPFtJ/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/tISchhPFtJ/concat.2.a.bcf /tmp/tISchhPFtJ/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/tISchhPFtJ/concat.3.a.vcf.gz /tmp/tISchhPFtJ/concat.3.b.vcf.gz /tmp/tISchhPFtJ/concat.3.0.vcf.gz /tmp/tISchhPFtJ/concat.3.c.vcf.gz /tmp/tISchhPFtJ/concat.3.d.vcf.gz /tmp/tISchhPFtJ/concat.3.e.vcf.gz /tmp/tISchhPFtJ/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/tISchhPFtJ/concat.3.a.vcf.gz /tmp/tISchhPFtJ/concat.3.b.vcf.gz /tmp/tISchhPFtJ/concat.3.0.vcf.gz /tmp/tISchhPFtJ/concat.3.c.vcf.gz /tmp/tISchhPFtJ/concat.3.d.vcf.gz /tmp/tISchhPFtJ/concat.3.e.vcf.gz /tmp/tISchhPFtJ/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/tISchhPFtJ/concat.3.a.bcf /tmp/tISchhPFtJ/concat.3.b.bcf /tmp/tISchhPFtJ/concat.3.0.bcf /tmp/tISchhPFtJ/concat.3.c.bcf /tmp/tISchhPFtJ/concat.3.d.bcf /tmp/tISchhPFtJ/concat.3.e.bcf /tmp/tISchhPFtJ/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/tISchhPFtJ/concat.3.a.bcf /tmp/tISchhPFtJ/concat.3.b.bcf /tmp/tISchhPFtJ/concat.3.0.bcf /tmp/tISchhPFtJ/concat.3.c.bcf /tmp/tISchhPFtJ/concat.3.d.bcf /tmp/tISchhPFtJ/concat.3.e.bcf /tmp/tISchhPFtJ/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 2994700552 .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/tISchhPFtJ/naive_concat.0.bcf /tmp/tISchhPFtJ/naive_concat.1.bcf /tmp/tISchhPFtJ/naive_concat.2.bcf /tmp/tISchhPFtJ/naive_concat.3.bcf /tmp/tISchhPFtJ/naive_concat.4.bcf /tmp/tISchhPFtJ/naive_concat.5.bcf /tmp/tISchhPFtJ/naive_concat.6.bcf /tmp/tISchhPFtJ/naive_concat.7.bcf /tmp/tISchhPFtJ/naive_concat.8.bcf /tmp/tISchhPFtJ/naive_concat.9.bcf | /<>/bcftools view -H .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/tISchhPFtJ/naive_concat.0.vcf.gz /tmp/tISchhPFtJ/naive_concat.1.vcf.gz /tmp/tISchhPFtJ/naive_concat.2.vcf.gz /tmp/tISchhPFtJ/naive_concat.3.vcf.gz /tmp/tISchhPFtJ/naive_concat.4.vcf.gz /tmp/tISchhPFtJ/naive_concat.5.vcf.gz /tmp/tISchhPFtJ/naive_concat.6.vcf.gz /tmp/tISchhPFtJ/naive_concat.7.vcf.gz /tmp/tISchhPFtJ/naive_concat.8.vcf.gz /tmp/tISchhPFtJ/naive_concat.9.vcf.gz | /<>/bcftools view -H .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/tISchhPFtJ/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tISchhPFtJ/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/tISchhPFtJ/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tISchhPFtJ/reheader.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/tISchhPFtJ/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tISchhPFtJ/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/tISchhPFtJ/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tISchhPFtJ/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/tISchhPFtJ/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tISchhPFtJ/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/tISchhPFtJ/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tISchhPFtJ/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/tISchhPFtJ/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tISchhPFtJ/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/tISchhPFtJ/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tISchhPFtJ/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/tISchhPFtJ/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tISchhPFtJ/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/tISchhPFtJ/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tISchhPFtJ/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /<>/test/empty.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/empty.vcf | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /tmp/tISchhPFtJ/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tISchhPFtJ/empty.bcf | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /tmp/tISchhPFtJ/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tISchhPFtJ/empty.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/tISchhPFtJ/rename.map -Ov /tmp/tISchhPFtJ/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/tISchhPFtJ/rename.map -Ob /tmp/tISchhPFtJ/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/tISchhPFtJ/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/tISchhPFtJ/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/tISchhPFtJ/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/convert.vcf.gz | /<>/bcftools convert -g -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/tISchhPFtJ/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/convert.vcf.gz | /<>/bcftools convert -g .,- 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/tISchhPFtJ/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/tISchhPFtJ/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/tISchhPFtJ/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/tISchhPFtJ/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/tISchhPFtJ/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/check.vcf.gz | /<>/bcftools convert -g -,. --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/tISchhPFtJ/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/check.vcf.gz | /<>/bcftools convert -g .,- --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/tISchhPFtJ/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/tISchhPFtJ/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/tISchhPFtJ/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/convert.vcf.gz | /<>/bcftools convert -h -,.,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/tISchhPFtJ/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/convert.vcf.gz | /<>/bcftools convert -h .,-,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/tISchhPFtJ/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/convert.vcf.gz | /<>/bcftools convert -h .,.,- 2>/dev/null .. ok test_vcf_convert_hls2vcf: /<>/bcftools convert -H /<>/test/convert.hls.gt.hap,/<>/test/convert.hls.gt.legend,/<>/test/convert.hls.gt.samples 2>/dev/null | grep -v ^## .. ok test_vcf_convert_hls2vcf: /<>/bcftools convert -H /<>/test/convert.hls.gt.hap,/<>/test/convert.hls.gt.legend,/<>/test/convert.hls.gt.samples -Ou 2>/dev/null | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples 2>/dev/null | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples -Ou 2>/dev/null | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/tISchhPFtJ/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/convert.vcf.gz | /<>/bcftools convert --hapsample -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/tISchhPFtJ/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tISchhPFtJ/convert.vcf.gz | /<>/bcftools convert --hapsample .,- 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools convert --no-version --gvcf2vcf -f /<>/test/gvcf.fa /tmp/tISchhPFtJ/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/tISchhPFtJ/convert.gvcf.vcf.gz | /<>/bcftools convert --gvcf2vcf -f /<>/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /<>/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.23andme 2>/dev/null .. ok test_vcf_convert_tsv2vcf: /<>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.23andme 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tISchhPFtJ/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/tISchhPFtJ/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/tISchhPFtJ/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/tISchhPFtJ/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tISchhPFtJ/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/tISchhPFtJ/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/tISchhPFtJ/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/tISchhPFtJ/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tISchhPFtJ/consensus.vcf.gz -f /<>/test/consensus.fa -i -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/tISchhPFtJ/consensus.vcf.gz -f /<>/test/consensus.fa -i -m /<>/test/consensus.tab -c /tmp/tISchhPFtJ/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/tISchhPFtJ/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tISchhPFtJ/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/tISchhPFtJ/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/tISchhPFtJ/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/tISchhPFtJ/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tISchhPFtJ/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tISchhPFtJ/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tISchhPFtJ/empty.vcf.gz -f /<>/test/consensus.fa 2>/dev/null .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -b /tmp/tISchhPFtJ/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/tISchhPFtJ/mpileup.bam.urllist 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -b /tmp/tISchhPFtJ/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/tISchhPFtJ/mpileup.cram.urllist 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_csq: /<>/bcftools csq -f /<>/test/csq.fa -g /<>/test/csq.gff3 /<>/test/csq.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq.gff3 ... Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000413103/ENST00000413103.fa -g /<>/test/csq/ENST00000413103/ENST00000413103.gff /<>/test/csq/ENST00000413103/long-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000413103/ENST00000413103.gff ... Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000357367/ENST00000357367.fa -g /<>/test/csq/ENST00000357367/ENST00000357367.gff /<>/test/csq/ENST00000357367/stop-retained.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000357367/ENST00000357367.gff ... Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000543077/ENST00000543077.fa -g /<>/test/csq/ENST00000543077/ENST00000543077.gff /<>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000543077/ENST00000543077.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000543077/ENST00000543077.fa -g /<>/test/csq/ENST00000543077/ENST00000543077.gff /<>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000543077/ENST00000543077.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000381157/ENST00000381157.fa -g /<>/test/csq/ENST00000381157/ENST00000381157.gff /<>/test/csq/ENST00000381157/haploid-diploid.vcf | /<>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' Parsing /<>/test/csq/ENST00000381157/ENST00000381157.gff ... Indexed 1 transcripts, 6 exons, 6 CDSs, 0 UTRs Calling... Warning: Skipping site with non-diploid/non-haploid genotypes at X:31180 C>T .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000593942/ENST00000593942.fa -g /<>/test/csq/ENST00000593942/ENST00000593942.gff /<>/test/csq/ENST00000593942/last-codon-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000593942/ENST00000593942.gff ... Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000301246/ENST00000301246.fa -g /<>/test/csq/ENST00000301246/ENST00000301246.gff /<>/test/csq/ENST00000301246/15bp-insert.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000301246/ENST00000301246.gff ... Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000536784/ENST00000536784.fa -g /<>/test/csq/ENST00000536784/ENST00000536784.gff /<>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000536784/ENST00000536784.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000536784/ENST00000536784.fa -g /<>/test/csq/ENST00000536784/ENST00000536784.gff /<>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000536784/ENST00000536784.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000520795/ENST00000520795.fa -g /<>/test/csq/ENST00000520795/ENST00000520795.gff /<>/test/csq/ENST00000520795/long-inside-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000520795/ENST00000520795.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000520795/ENST00000520795.fa -g /<>/test/csq/ENST00000520795/ENST00000520795.gff /<>/test/csq/ENST00000520795/long-inside-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000520795/ENST00000520795.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000557788/ENST00000557788.fa -g /<>/test/csq/ENST00000557788/ENST00000557788.gff /<>/test/csq/ENST00000557788/long-overlap-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000557788/ENST00000557788.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000368801/ENST00000368801.fa -g /<>/test/csq/ENST00000368801/ENST00000368801.gff /<>/test/csq/ENST00000368801/compound-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000368801/ENST00000368801.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000448695/ENST00000448695.fa -g /<>/test/csq/ENST00000448695/ENST00000448695.gff /<>/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000448695/ENST00000448695.gff ... Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000410009/ENST00000410009.fa -g /<>/test/csq/ENST00000410009/ENST00000410009.gff /<>/test/csq/ENST00000410009/frameshift.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000410009/ENST00000410009.gff ... Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000318249/ENST00000318249.fa -g /<>/test/csq/ENST00000318249/ENST00000318249.gff /<>/test/csq/ENST00000318249/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000318249/ENST00000318249.gff ... Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000318249/ENST00000318249.fa -g /<>/test/csq/ENST00000318249/ENST00000318249.gff /<>/test/csq/ENST00000318249/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000318249/ENST00000318249.gff ... Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000420670/ENST00000420670.fa -g /<>/test/csq/ENST00000420670/ENST00000420670.gff /<>/test/csq/ENST00000420670/start-stop-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000420670/ENST00000420670.gff ... Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000545279/ENST00000545279.fa -g /<>/test/csq/ENST00000545279/ENST00000545279.gff /<>/test/csq/ENST00000545279/splice-region-insert.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000545279/ENST00000545279.gff ... Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000573314/ENST00000573314.fa -g /<>/test/csq/ENST00000573314/ENST00000573314.gff /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000573314/ENST00000573314.gff ... Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000573314/ENST00000573314.fa -g /<>/test/csq/ENST00000573314/ENST00000573314.gff /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000573314/ENST00000573314.gff ... Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENSG00000173376/ENSG00000173376.fa -g /<>/test/csq/ENSG00000173376/ENSG00000173376.gff /<>/test/csq/ENSG00000173376/synon.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENSG00000173376/ENSG00000173376.gff ... Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000479739/ENST00000479739.fa -g /<>/test/csq/ENST00000479739/ENST00000479739.gff /<>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000479739/ENST00000479739.gff ... Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000479739/ENST00000479739.fa -g /<>/test/csq/ENST00000479739/ENST00000479739.gff /<>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000479739/ENST00000479739.gff ... Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000390520/ENST00000390520.fa -g /<>/test/csq/ENST00000390520/ENST00000390520.gff /<>/test/csq/ENST00000390520/deletion-overlap.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000390520/ENST00000390520.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000303039/ENST00000303039.fa -g /<>/test/csq/ENST00000303039/ENST00000303039.gff /<>/test/csq/ENST00000303039/not-a-stop.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000303039/ENST00000303039.fa -g /<>/test/csq/ENST00000303039/ENST00000303039.gff /<>/test/csq/ENST00000303039/not-a-stop.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000373833/ENST00000373833.fa -g /<>/test/csq/ENST00000373833/ENST00000373833.gff /<>/test/csq/ENST00000373833/boundary-insertion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000373833/ENST00000373833.gff ... Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000373833/ENST00000373833.fa -g /<>/test/csq/ENST00000373833/ENST00000373833.gff /<>/test/csq/ENST00000373833/boundary-insertion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000373833/ENST00000373833.gff ... Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000528237/ENST00000528237.fa -g /<>/test/csq/ENST00000528237/ENST00000528237.gff /<>/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000528237/ENST00000528237.gff ... Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000436063/ENST00000436063.fa -g /<>/test/csq/ENST00000436063/ENST00000436063.gff /<>/test/csq/ENST00000436063/insert-before-utr.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000436063/ENST00000436063.gff ... Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000382647/ENST00000382647.fa -g /<>/test/csq/ENST00000382647/ENST00000382647.gff /<>/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000382647/ENST00000382647.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000218032/ENST00000218032.fa -g /<>/test/csq/ENST00000218032/ENST00000218032.gff /<>/test/csq/ENST00000218032/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000218032/ENST00000218032.fa -g /<>/test/csq/ENST00000218032/ENST00000218032.gff /<>/test/csq/ENST00000218032/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000409523/ENST00000409523.fa -g /<>/test/csq/ENST00000409523/ENST00000409523.gff /<>/test/csq/ENST00000409523/long-overlapping-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000409523/ENST00000409523.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000519442/ENST00000519442.fa -g /<>/test/csq/ENST00000519442/ENST00000519442.gff /<>/test/csq/ENST00000519442/synon-splice-region-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000519442/ENST00000519442.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000295641/ENST00000295641.fa -g /<>/test/csq/ENST00000295641/ENST00000295641.gff /<>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000295641/ENST00000295641.gff ... Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000295641/ENST00000295641.fa -g /<>/test/csq/ENST00000295641/ENST00000295641.gff /<>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000295641/ENST00000295641.gff ... Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000375992/ENST00000375992.fa -g /<>/test/csq/ENST00000375992/ENST00000375992.gff /<>/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000375992/ENST00000375992.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000294661/ENST00000294661.fa -g /<>/test/csq/ENST00000294661/ENST00000294661.gff /<>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000294661/ENST00000294661.fa -g /<>/test/csq/ENST00000294661/ENST00000294661.gff /<>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000329454/ENST00000329454.fa -g /<>/test/csq/ENST00000329454/ENST00000329454.gff /<>/test/csq/ENST00000329454/boundary-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000329454/ENST00000329454.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000329454/ENST00000329454.fa -g /<>/test/csq/ENST00000329454/ENST00000329454.gff /<>/test/csq/ENST00000329454/boundary-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000329454/ENST00000329454.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000520868/ENST00000520868.fa -g /<>/test/csq/ENST00000520868/ENST00000520868.gff /<>/test/csq/ENST00000520868/long-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000520868/ENST00000520868.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000378322/ENST00000378322.fa -g /<>/test/csq/ENST00000378322/ENST00000378322.gff /<>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000378322/ENST00000378322.fa -g /<>/test/csq/ENST00000378322/ENST00000378322.gff /<>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/insert3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/insert3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/snps.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/snps.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000624631/ENST00000624631.fa -g /<>/test/csq/ENST00000624631/ENST00000624631.gff /<>/test/csq/ENST00000624631/ambiguous.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000624631/ENST00000624631.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000542803/ENST00000542803.fa -g /<>/test/csq/ENST00000542803/ENST00000542803.gff /<>/test/csq/ENST00000542803/splice-region.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000542803/ENST00000542803.gff ... Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000542803/ENST00000542803.fa -g /<>/test/csq/ENST00000542803/ENST00000542803.gff /<>/test/csq/ENST00000542803/splice-region.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000542803/ENST00000542803.gff ... Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000227471/ENST00000227471.fa -g /<>/test/csq/ENST00000227471/ENST00000227471.gff /<>/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000227471/ENST00000227471.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000256452/ENST00000256452.fa -g /<>/test/csq/ENST00000256452/ENST00000256452.gff /<>/test/csq/ENST00000256452/intron.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000256452/ENST00000256452.gff ... Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs Calling... .. ok Number of tests: total .. 617 passed .. 561 failed .. 56 Makefile:121: recipe for target 'test' failed make[1]: *** [test] Error 1 make[1]: Leaving directory '/<>' dh_auto_test: make -j4 test returned exit code 2 debian/rules:11: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 20170730-1714 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 20876 Build-Time: 80 Distribution: artful-proposed Fail-Stage: build Host Architecture: i386 Install-Time: 15 Job: bcftools_1.4.1-3.dsc Machine Architecture: amd64 Package: bcftools Package-Time: 95 Source-Version: 1.4.1-3 Space: 20876 Status: attempted Version: 1.4.1-3 -------------------------------------------------------------------------------- Finished at 20170730-1714 Build needed 00:01:35, 20876k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-13171782'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-13171782/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-13171782'] Unmounting chroot for build PACKAGEBUILD-13171782... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-13171782'] Removing build PACKAGEBUILD-13171782