RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-06 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 21:17:51 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_151 python-lpbuildd_151 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.2 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 9 Sep 09:40:46 ntpdate[1781]: adjust time server 10.211.37.1 offset -0.004589 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13205066 /home/buildd/filecache-default/7fe38ae672de2c40a7e6ba74a0e6690544a5bb48 Creating target for build PACKAGEBUILD-13205066 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13205066 Starting target for build PACKAGEBUILD-13205066 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13205066 '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-13205066 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13205066 Updating target for build PACKAGEBUILD-13205066 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 [1122 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [550 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe i386 Packages [8170 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4777 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main i386 Packages [131 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [48.5 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe i386 Packages [122 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [62.4 kB] Fetched 15.6 MB in 7s (2222 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: g++-6 libperl5.24 libstdc++-6-dev perl-modules-5.24 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: binutils-common binutils-i686-linux-gnu cpp-7 fdisk g++-7 gcc-7 gcc-7-base libasan4 libbinutils libgcc-7-dev libperl5.26 libstdc++-7-dev 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 diffutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-6 gcc gcc-6 gcc-6-base grep init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libassuan0 libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcilkrts5 libcomerr2 libcryptsetup4 libcurl3-gnutls 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 libmpfr4 libmpx2 libnpth0 libp11-kit0 libpcre3 libpng16-16 libpsl5 libquadmath0 libroken18-heimdal libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 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 sensible-utils systemd systemd-sysv tar tzdata util-linux xz-utils zlib1g 117 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. Need to get 166 MB of archives. After this operation, 465 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-modules-5.26 all 5.26.0-7 [2762 kB] Get:3 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libperl5.26 i386 5.26.0-7 [3159 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed/main i386 perl i386 5.26.0-7 [202 kB] Get:5 http://ftpmaster.internal/ubuntu artful-proposed/main i386 perl-base i386 5.26.0-7 [1492 kB] Get:6 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libc6-dev i386 2.26-0ubuntu1 [2145 kB] Get:7 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libc-dev-bin i386 2.26-0ubuntu1 [67.0 kB] Get:8 http://ftpmaster.internal/ubuntu artful-proposed/main i386 linux-libc-dev i386 4.12.0-13.14 [960 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libc6 i386 2.26-0ubuntu1 [2547 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libc-bin i386 2.26-0ubuntu1 [572 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/main i386 gcc-7-base i386 7.2.0-4ubuntu1 [17.9 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libgcc1 i386 1:7.2.0-4ubuntu1 [47.0 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main i386 libdb5.3 i386 5.3.28-13.1 [738 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main i386 zlib1g i386 1:1.2.11.dfsg-0ubuntu2 [58.2 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main i386 init-system-helpers all 1.49ubuntu1 [36.4 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 debianutils i386 4.8.2 [86.5 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main i386 bash i386 4.4-5ubuntu1 [622 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main i386 bsdutils i386 1:2.30.1-0ubuntu4 [62.4 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main i386 diffutils i386 1:3.6-1 [175 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 e2fslibs i386 1.43.5-1 [183 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main i386 e2fsprogs i386 1.43.5-1 [533 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main i386 findutils i386 4.6.0+git+20170729-2 [305 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main i386 grep i386 3.1-2 [163 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main i386 login i386 1:4.2-3.2ubuntu4 [307 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main i386 libuuid1 i386 2.30.1-0ubuntu4 [15.7 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main i386 libblkid1 i386 2.30.1-0ubuntu4 [133 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main i386 libpcre3 i386 2:8.39-4 [227 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main i386 libselinux1 i386 2.6-3build2 [72.8 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main i386 libmount1 i386 2.30.1-0ubuntu4 [143 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main i386 libsmartcols1 i386 2.30.1-0ubuntu4 [85.4 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main i386 libfdisk1 i386 2.30.1-0ubuntu4 [173 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main i386 fdisk i386 2.30.1-0ubuntu4 [115 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main i386 util-linux i386 2.30.1-0ubuntu4 [903 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main i386 mount i386 2.30.1-0ubuntu4 [115 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main i386 liblzma5 i386 5.2.2-1.3 [98.5 kB] Get:39 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libstdc++6 i386 7.2.0-4ubuntu1 [437 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main i386 libapt-pkg5.0 i386 1.5~rc1~ubuntu1 [849 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 libp11-kit0 i386 0.23.7-3 [188 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main i386 libgnutls30 i386 3.5.8-6ubuntu3 [695 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main i386 libk5crypto3 i386 1.15.1-2 [88.3 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main i386 libgssapi-krb5-2 i386 1.15.1-2 [129 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main i386 libkrb5-3 i386 1.15.1-2 [300 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main i386 libkrb5support0 i386 1.15.1-2 [34.0 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main i386 libcomerr2 i386 1.43.5-1 [11.0 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main i386 libidn2-0 i386 2.0.2-3 [92.7 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main i386 libldap-2.4-2 i386 2.4.45+dfsg-1ubuntu1 [167 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main i386 libldap-common all 2.4.45+dfsg-1ubuntu1 [16.6 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main i386 libroken18-heimdal i386 7.4.0.dfsg.1-2 [44.5 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main i386 libasn1-8-heimdal i386 7.4.0.dfsg.1-2 [187 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main i386 libheimbase1-heimdal i386 7.4.0.dfsg.1-2 [32.0 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main i386 libhcrypto4-heimdal i386 7.4.0.dfsg.1-2 [93.3 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main i386 libwind0-heimdal i386 7.4.0.dfsg.1-2 [49.1 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main i386 libhx509-5-heimdal i386 7.4.0.dfsg.1-2 [118 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main i386 libsqlite3-0 i386 3.19.3-3 [525 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main i386 libkrb5-26-heimdal i386 7.4.0.dfsg.1-2 [231 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main i386 libheimntlm0-heimdal i386 7.4.0.dfsg.1-2 [16.6 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main i386 libgssapi3-heimdal i386 7.4.0.dfsg.1-2 [108 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main i386 libsasl2-modules-db i386 2.1.27~101-g0780600+dfsg-3ubuntu1 [15.5 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main i386 libsasl2-2 i386 2.1.27~101-g0780600+dfsg-3ubuntu1 [52.7 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main i386 libpsl5 i386 0.18.0-2 [41.3 kB] Get:65 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libcurl3-gnutls i386 7.55.1-1ubuntu1 [214 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main i386 apt-transport-https i386 1.5~rc1~ubuntu1 [39.0 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main i386 apt i386 1.5~rc1~ubuntu1 [1147 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main i386 libip4tc0 i386 1.6.1-2ubuntu1 [20.5 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main i386 libapparmor1 i386 2.11.0-2ubuntu16 [30.3 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main i386 libaudit-common all 1:2.7.7-1ubuntu2 [3998 B] Get:71 http://ftpmaster.internal/ubuntu artful/main i386 libcap-ng0 i386 0.7.7-3build1 [11.1 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main i386 libaudit1 i386 1:2.7.7-1ubuntu2 [39.3 kB] Get:73 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libudev1 i386 234-2ubuntu10 [56.2 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main i386 libdevmapper1.02.1 i386 2:1.02.137-2ubuntu3 [145 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main i386 libgpg-error0 i386 1.27-3 [39.4 kB] Get:76 http://ftpmaster.internal/ubuntu artful/main i386 libgcrypt20 i386 1.7.8-2 [375 kB] Get:77 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libcryptsetup4 i386 2:1.7.3-4ubuntu1 [85.1 kB] Get:78 http://ftpmaster.internal/ubuntu artful/main i386 libkmod2 i386 24-1ubuntu2 [46.3 kB] Get:79 http://ftpmaster.internal/ubuntu artful-proposed/main i386 systemd i386 234-2ubuntu10 [2873 kB] Get:80 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libsystemd0 i386 234-2ubuntu10 [228 kB] Get:81 http://ftpmaster.internal/ubuntu artful/main i386 init i386 1.49ubuntu1 [5438 B] Get:82 http://ftpmaster.internal/ubuntu artful-proposed/main i386 systemd-sysv i386 234-2ubuntu10 [11.9 kB] Get:83 http://ftpmaster.internal/ubuntu artful/main i386 libsemanage-common all 2.6-2build2 [6682 B] Get:84 http://ftpmaster.internal/ubuntu artful/main i386 libsemanage1 i386 2.6-2build2 [90.4 kB] Get:85 http://ftpmaster.internal/ubuntu artful/main i386 libss2 i386 1.43.5-1 [11.5 kB] Get:86 http://ftpmaster.internal/ubuntu artful/main i386 passwd i386 1:4.2-3.2ubuntu4 [790 kB] Get:87 http://ftpmaster.internal/ubuntu artful/main i386 sensible-utils all 0.0.10 [14.6 kB] Get:88 http://ftpmaster.internal/ubuntu artful/main i386 dmsetup i386 2:1.02.137-2ubuntu3 [73.2 kB] Get:89 http://ftpmaster.internal/ubuntu artful/main i386 libassuan0 i386 2.4.3-3 [36.7 kB] Get:90 http://ftpmaster.internal/ubuntu artful/main i386 libnpth0 i386 1.5-2 [7942 B] Get:91 http://ftpmaster.internal/ubuntu artful/main i386 libssl1.0.0 i386 1.0.2g-1ubuntu13 [910 kB] Get:92 http://ftpmaster.internal/ubuntu artful-proposed/main i386 multiarch-support i386 2.26-0ubuntu1 [6828 B] Get:93 http://ftpmaster.internal/ubuntu artful/main i386 tzdata all 2017b-2 [203 kB] Get:94 http://ftpmaster.internal/ubuntu artful/main i386 xz-utils i386 5.2.2-1.3 [88.6 kB] Get:95 http://ftpmaster.internal/ubuntu artful/main i386 openssl i386 1.0.2g-1ubuntu13 [506 kB] Get:96 http://ftpmaster.internal/ubuntu artful/main i386 ca-certificates all 20170717 [167 kB] Get:97 http://ftpmaster.internal/ubuntu artful/main i386 libpng16-16 i386 1.6.32-1 [185 kB] Get:98 http://ftpmaster.internal/ubuntu artful/main i386 advancecomp i386 2.0-1 [206 kB] Get:99 http://ftpmaster.internal/ubuntu artful-proposed/main i386 binutils i386 2.29-9ubuntu1 [30.5 kB] Get:100 http://ftpmaster.internal/ubuntu artful-proposed/main i386 binutils-common i386 2.29-9ubuntu1 [37.9 kB] Get:101 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libbinutils i386 2.29-9ubuntu1 [549 kB] Get:102 http://ftpmaster.internal/ubuntu artful-proposed/main i386 binutils-i686-linux-gnu i386 2.29-9ubuntu1 [2127 kB] Get:103 http://ftpmaster.internal/ubuntu artful/main i386 libmpfr4 i386 3.1.6-1 [194 kB] Get:104 http://ftpmaster.internal/ubuntu artful-proposed/main i386 cpp-7 i386 7.2.0-4ubuntu1 [31.8 MB] Get:105 http://ftpmaster.internal/ubuntu artful/main i386 cpp i386 4:7.1.0-1ubuntu3 [27.6 kB] Get:106 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libquadmath0 i386 7.2.0-4ubuntu1 [205 kB] Get:107 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libitm1 i386 7.2.0-4ubuntu1 [30.3 kB] Get:108 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libmpx2 i386 7.2.0-4ubuntu1 [13.0 kB] Get:109 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libubsan0 i386 7.2.0-4ubuntu1 [134 kB] Get:110 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libcilkrts5 i386 7.2.0-4ubuntu1 [47.3 kB] Get:111 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libgomp1 i386 7.2.0-4ubuntu1 [80.3 kB] Get:112 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libatomic1 i386 7.2.0-4ubuntu1 [9700 B] Get:113 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libasan3 i386 6.4.0-5ubuntu3 [308 kB] Get:114 http://ftpmaster.internal/ubuntu artful-proposed/universe i386 g++-6 i386 6.4.0-5ubuntu3 [7645 kB] Get:115 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libstdc++-6-dev i386 6.4.0-5ubuntu3 [1475 kB] Get:116 http://ftpmaster.internal/ubuntu artful-proposed/main i386 gcc-6 i386 6.4.0-5ubuntu3 [7487 kB] Get:117 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libgcc-6-dev i386 6.4.0-5ubuntu3 [2332 kB] Get:118 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libcc1-0 i386 7.2.0-4ubuntu1 [41.4 kB] Get:119 http://ftpmaster.internal/ubuntu artful-proposed/main i386 cpp-6 i386 6.4.0-5ubuntu3 [6817 kB] Get:120 http://ftpmaster.internal/ubuntu artful-proposed/main i386 gcc-6-base i386 6.4.0-5ubuntu3 [16.8 kB] Get:121 http://ftpmaster.internal/ubuntu artful/main i386 dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:122 http://ftpmaster.internal/ubuntu artful/main i386 libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:123 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libasan4 i386 7.2.0-4ubuntu1 [354 kB] Get:124 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libgcc-7-dev i386 7.2.0-4ubuntu1 [2383 kB] Get:125 http://ftpmaster.internal/ubuntu artful-proposed/main i386 gcc-7 i386 7.2.0-4ubuntu1 [31.3 MB] Get:126 http://ftpmaster.internal/ubuntu artful/main i386 gcc i386 4:7.1.0-1ubuntu3 [5336 B] Get:127 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libstdc++-7-dev i386 7.2.0-4ubuntu1 [1496 kB] Get:128 http://ftpmaster.internal/ubuntu artful-proposed/main i386 g++-7 i386 7.2.0-4ubuntu1 [34.1 MB] Get:129 http://ftpmaster.internal/ubuntu artful/main i386 g++ i386 4:7.1.0-1ubuntu3 [1490 B] Get:130 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 166 MB in 16s (9794 kB/s) (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 ... 12465 files and directories currently installed.) Preparing to unpack .../debconf_1.5.63_all.deb ... Unpacking debconf (1.5.63) over (1.5.60ubuntu1) ... Setting up debconf (1.5.63) ... (Reading database ... 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Setting up util-linux (2.30.1-0ubuntu4) ... update-alternatives: warning: alternative /usr/bin/pg (part of link group pager) doesn't exist; removing from list of alternatives Setting up mount (2.30.1-0ubuntu4) ... Setting up systemd (234-2ubuntu10) ... 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. Created symlink /etc/systemd/system/dbus-org.freedesktop.network1.service -> /lib/systemd/system/systemd-networkd.service. Created symlink /etc/systemd/system/multi-user.target.wants/systemd-networkd.service -> /lib/systemd/system/systemd-networkd.service. Created symlink /etc/systemd/system/sockets.target.wants/systemd-networkd.socket -> /lib/systemd/system/systemd-networkd.socket. Created symlink /etc/systemd/system/network-online.target.wants/systemd-networkd-wait-online.service -> /lib/systemd/system/systemd-networkd-wait-online.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 ... (Reading database ... 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Preparing to unpack .../38-gcc_4%3a7.1.0-1ubuntu3_i386.deb ... Removing old gcc doc directory. Unpacking gcc (4:7.1.0-1ubuntu3) over (4:6.3.0-2ubuntu1) ... Selecting previously unselected package libstdc++-7-dev:i386. Preparing to unpack .../39-libstdc++-7-dev_7.2.0-4ubuntu1_i386.deb ... Unpacking libstdc++-7-dev:i386 (7.2.0-4ubuntu1) ... Selecting previously unselected package g++-7. Preparing to unpack .../40-g++-7_7.2.0-4ubuntu1_i386.deb ... Unpacking g++-7 (7.2.0-4ubuntu1) ... Preparing to unpack .../41-g++_4%3a7.1.0-1ubuntu3_i386.deb ... Unpacking g++ (4:7.1.0-1ubuntu3) over (4:6.3.0-2ubuntu1) ... Preparing to unpack .../42-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 (7.2.0-4ubuntu1) ... Setting up libnpth0:i386 (1.5-2) ... Setting up libgomp1:i386 (7.2.0-4ubuntu1) ... Setting up libatomic1:i386 (7.2.0-4ubuntu1) ... Setting up libcc1-0:i386 (7.2.0-4ubuntu1) ... Setting up libidn2-0:i386 (2.0.2-3) ... Setting up libssl1.0.0:i386 (1.0.2g-1ubuntu13) ... Setting up libasan4:i386 (7.2.0-4ubuntu1) ... Setting up libpng16-16:i386 (1.6.32-1) ... Setting up libldap-common (2.4.45+dfsg-1ubuntu1) ... Setting up libcilkrts5:i386 (7.2.0-4ubuntu1) ... Setting up libpsl5:i386 (0.18.0-2) ... Setting up multiarch-support (2.26-0ubuntu1) ... Setting up tzdata (2017b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Sep 9 09:42:14 UTC 2017. Universal Time is now: Sat Sep 9 09:42:14 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (234-2ubuntu10) ... Setting up libubsan0:i386 (7.2.0-4ubuntu1) ... Setting up gcc-6-base:i386 (6.4.0-5ubuntu3) ... Setting up libsasl2-modules-db:i386 (2.1.27~101-g0780600+dfsg-3ubuntu1) ... Setting up linux-libc-dev:i386 (4.12.0-13.14) ... Setting up advancecomp (2.0-1) ... Setting up libsasl2-2:i386 (2.1.27~101-g0780600+dfsg-3ubuntu1) ... Setting up libroken18-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up perl-modules-5.26 (5.26.0-7) ... Setting up libkrb5support0:i386 (1.15.1-2) ... Setting up binutils-common:i386 (2.29-9ubuntu1) ... Setting up libmpx2:i386 (7.2.0-4ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu1) ... Setting up libperl5.26:i386 (5.26.0-7) ... 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 libmpfr4:i386 (3.1.6-1) ... Setting up dmsetup (2:1.02.137-2ubuntu3) ... Setting up cpp-6 (6.4.0-5ubuntu3) ... Setting up libc-dev-bin (2.26-0ubuntu1) ... Setting up ca-certificates (20170717) ... Updating certificates in /etc/ssl/certs... 7 added, 32 removed; done. Setting up libc6-dev:i386 (2.26-0ubuntu1) ... Setting up libassuan0:i386 (2.4.3-3) ... Setting up libusb-0.1-4:i386 (2:0.1.12-31) ... Setting up libitm1:i386 (7.2.0-4ubuntu1) ... Setting up libk5crypto3:i386 (1.15.1-2) ... Setting up libasan3:i386 (6.4.0-5ubuntu3) ... Setting up libgcc-6-dev:i386 (6.4.0-5ubuntu3) ... Setting up libstdc++-6-dev:i386 (6.4.0-5ubuntu3) ... Setting up libwind0-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up libbinutils:i386 (2.29-9ubuntu1) ... Setting up init (1.49ubuntu1) ... 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 libgcc-7-dev:i386 (7.2.0-4ubuntu1) ... Setting up cpp-7 (7.2.0-4ubuntu1) ... Setting up libstdc++-7-dev:i386 (7.2.0-4ubuntu1) ... Setting up perl (5.26.0-7) ... update-alternatives: warning: alternative /usr/bin/prename (part of link group rename) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/rename is dangling; it will be updated with best choice 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 cpp (4:7.1.0-1ubuntu3) ... Setting up libdpkg-perl (1.18.24ubuntu1) ... Setting up libgssapi-krb5-2:i386 (1.15.1-2) ... Setting up libgssapi3-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up libldap-2.4-2:i386 (2.4.45+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:i386 (7.55.1-1ubuntu1) ... Setting up apt-transport-https (1.5~rc1~ubuntu1) ... Setting up binutils-i686-linux-gnu (2.29-9ubuntu1) ... Setting up binutils (2.29-9ubuntu1) ... Setting up gcc-7 (7.2.0-4ubuntu1) ... Setting up g++-7 (7.2.0-4ubuntu1) ... Setting up gcc (4:7.1.0-1ubuntu3) ... Setting up gcc-6 (6.4.0-5ubuntu3) ... Setting up g++-6 (6.4.0-5ubuntu3) ... Setting up dpkg-dev (1.18.24ubuntu1) ... Setting up g++ (4:7.1.0-1ubuntu3) ... Processing triggers for libc-bin (2.26-0ubuntu1) ... Processing triggers for ca-certificates (20170717) ... 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 PACKAGEBUILD-13205066 i386 artful-proposed -c chroot:build-PACKAGEBUILD-13205066 --arch=i386 --dist=artful-proposed --nolog bcftools_1.4.1-3build1.dsc Initiating build PACKAGEBUILD-13205066 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 21:17:51 UTC 2017 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-06.buildd +==============================================================================+ | bcftools 1.4.1-3build1 (i386) 09 Sep 2017 09:42 | +==============================================================================+ Package: bcftools Version: 1.4.1-3build1 Source Version: 1.4.1-3build1 Distribution: artful-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/bcftools-FYPoPS/bcftools-1.4.1' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-FYPoPS' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13205066/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bcftools_1.4.1-3build1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-RREB_W/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-RREB_W/apt_archive ./ InRelease Get:2 copy:/<>/resolver-RREB_W/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-RREB_W/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-RREB_W/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-RREB_W/apt_archive ./ Packages [524 B] Fetched 2857 B in 0s (161 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: g++-6 libperl5.24 libstdc++-6-dev perl-modules-5.24 Use '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 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-RREB_W/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 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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-V4XQrm/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. Ign:1 copy:/<>/resolver-V4XQrm/apt_archive ./ InRelease Get:2 copy:/<>/resolver-V4XQrm/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-V4XQrm/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-V4XQrm/apt_archive ./ Sources [247 B] Get:5 copy:/<>/resolver-V4XQrm/apt_archive ./ Packages [565 B] Fetched 2931 B in 0s (160 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: g++-6 libperl5.24 libstdc++-6-dev perl-modules-5.24 Use '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 libgsl23 libgslcblas0 libhts-dev libhts2 libicu57 libio-pty-perl liblzma-dev libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libhts-dev libhts2 libicu57 libio-pty-perl liblzma-dev libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 39 newly installed, 1 to remove and 0 not upgraded. Need to get 19.9 MB of archives. After this operation, 76.3 MB of additional disk space will be used. Get:1 copy:/<>/resolver-V4XQrm/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [820 B] Get:2 http://ftpmaster.internal/ubuntu artful/main i386 groff-base i386 1.22.3-9 [1163 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main i386 libbsd0 i386 0.8.6-1 [45.1 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main i386 bsdmainutils i386 9.0.12+nmu1ubuntu1 [181 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main i386 libpipeline1 i386 1.4.2-1 [26.8 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main i386 man-db i386 2.7.6.1-2 [906 kB] Get:7 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libmagic-mgc i386 1:5.32-1 [184 kB] Get:8 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libmagic1 i386 1:5.32-1 [75.0 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main i386 file i386 1:5.32-1 [21.9 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main i386 gettext-base i386 0.19.8.1-4ubuntu1 [50.7 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libglib2.0-0 i386 2.53.6-1ubuntu2 [1231 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main i386 libicu57 i386 57.1-6 [7837 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main i386 libxml2 i386 2.9.4+dfsg1-3.1 [705 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main i386 libsigsegv2 i386 2.11-1 [13.5 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main i386 m4 i386 1.4.18-1 [196 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main i386 autoconf all 2.69-11 [322 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main i386 autotools-dev all 20161112.1 [39.5 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main i386 automake all 1:1.15-6ubuntu1 [509 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main i386 autopoint all 0.19.8.1-4ubuntu1 [412 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main i386 libtool all 2.4.6-2 [194 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main i386 dh-autoreconf all 14 [15.5 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main i386 libarchive-zip-perl all 1.59-1 [84.0 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main i386 libfile-stripnondeterminism-perl all 0.038-1 [13.3 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main i386 libtimedate-perl all 2.3000-2 [37.5 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main i386 dh-strip-nondeterminism all 0.038-1 [5026 B] Get:26 http://ftpmaster.internal/ubuntu artful/main i386 libcroco3 i386 0.6.12-1 [87.5 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main i386 gettext i386 0.19.8.1-4ubuntu1 [1097 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main i386 po-debconf all 1.0.20 [232 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main i386 debhelper all 10.7.2ubuntu2 [877 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main i386 libgslcblas0 i386 2.4+dfsg-6 [80.5 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main i386 libgsl23 i386 2.4+dfsg-6 [802 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main i386 libgsl-dev i386 2.4+dfsg-6 [1042 kB] Get:34 http://ftpmaster.internal/ubuntu artful/universe i386 libhts2 i386 1.5-1 [304 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main i386 liblzma-dev i386 5.2.2-1.3 [154 kB] Get:36 http://ftpmaster.internal/ubuntu artful/universe i386 tabix i386 1.5-1 [335 kB] Get:37 http://ftpmaster.internal/ubuntu artful/universe i386 libhts-dev i386 1.5-1 [411 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main i386 libio-pty-perl i386 1:1.08-1.1build4 [30.8 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main i386 zlib1g-dev i386 1:1.2.11.dfsg-0ubuntu2 [178 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.9 MB in 0s (28.4 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 ... 15448 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_i386.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../01-libbsd0_0.8.6-1_i386.deb ... Unpacking libbsd0:i386 (0.8.6-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_9.0.12+nmu1ubuntu1_i386.deb ... 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Setting up libarchive-zip-perl (1.59-1) ... Setting up libio-pty-perl (1:1.08-1.1build4) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:i386 (2.11-1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:i386 (2.53.6-1ubuntu2) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-4ubuntu1) ... Setting up libpipeline1:i386 (1.4.2-1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:i386 (57.1-6) ... Setting up libbsd0:i386 (0.8.6-1) ... Setting up libxml2:i386 (2.9.4+dfsg1-3.1) ... Setting up libmagic-mgc (1:5.32-1) ... Setting up libmagic1:i386 (1:5.32-1) ... Setting up libcroco3:i386 (0.6.12-1) ... Processing triggers for libc-bin (2.26-0ubuntu1) ... Setting up autotools-dev (20161112.1) ... Setting up tabix (1.5-1) ... Setting up liblzma-dev:i386 (5.2.2-1.3) ... Setting up bsdmainutils (9.0.12+nmu1ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgslcblas0:i386 (2.4+dfsg-6) ... Setting up libhts2:i386 (1.5-1) ... Setting up autopoint (0.19.8.1-4ubuntu1) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.038-1) ... Setting up libgsl23:i386 (2.4+dfsg-6) ... Setting up gettext (0.19.8.1-4ubuntu1) ... Setting up libgsl-dev (2.4+dfsg-6) ... Setting up libhts-dev:i386 (1.5-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.038-1) ... Setting up debhelper (10.7.2ubuntu2) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... (Reading database ... (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 ... 17709 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.26-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-93-generic amd64 (i686) Toolchain package versions: binutils_2.29-9ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.4.0-5ubuntu3 g++-7_7.2.0-4ubuntu1 gcc-6_6.4.0-5ubuntu3 gcc-7_7.2.0-4ubuntu1 libc6-dev_2.26-0ubuntu1 libstdc++-6-dev_6.4.0-5ubuntu3 libstdc++-7-dev_7.2.0-4ubuntu1 libstdc++6_7.2.0-4ubuntu1 linux-libc-dev_4.12.0-13.14 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.5~rc1~ubuntu1 apt-transport-https_1.5~rc1~ubuntu1 autoconf_2.69-11 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-4ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu101 base-passwd_3.5.43 bash_4.4-5ubuntu1 binutils_2.29-9ubuntu1 binutils-common_2.29-9ubuntu1 binutils-i686-linux-gnu_2.29-9ubuntu1 bsdmainutils_9.0.12+nmu1ubuntu1 bsdutils_1:2.30.1-0ubuntu4 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.26-3ubuntu3 cpp_4:7.1.0-1ubuntu3 cpp-6_6.4.0-5ubuntu3 cpp-7_7.2.0-4ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.63 debhelper_10.7.2ubuntu2 debianutils_4.8.2 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dmsetup_2:1.02.137-2ubuntu3 dpkg_1.18.24ubuntu1 dpkg-dev_1.18.24ubuntu1 e2fslibs_1.43.5-1 e2fsprogs_1.43.5-1 fakeroot_1.21-1ubuntu2 fdisk_2.30.1-0ubuntu4 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.1.0-1ubuntu3 g++-6_6.4.0-5ubuntu3 g++-7_7.2.0-4ubuntu1 gcc_4:7.1.0-1ubuntu3 gcc-6_6.4.0-5ubuntu3 gcc-6-base_6.4.0-5ubuntu3 gcc-7_7.2.0-4ubuntu1 gcc-7-base_7.2.0-4ubuntu1 gettext_0.19.8.1-4ubuntu1 gettext-base_0.19.8.1-4ubuntu1 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_1.49ubuntu1 init-system-helpers_1.49ubuntu1 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu16 libapt-pkg5.0_1.5~rc1~ubuntu1 libarchive-zip-perl_1.59-1 libasan3_6.4.0-5ubuntu3 libasan4_7.2.0-4ubuntu1 libasn1-8-heimdal_7.4.0.dfsg.1-2 libassuan0_2.4.3-3 libatomic1_7.2.0-4ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.7.7-1ubuntu2 libaudit1_1:2.7.7-1ubuntu2 libbinutils_2.29-9ubuntu1 libblkid1_2.30.1-0ubuntu4 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.26-0ubuntu1 libc-dev-bin_2.26-0ubuntu1 libc6_2.26-0ubuntu1 libc6-dev_2.26-0ubuntu1 libcap-ng0_0.7.7-3build1 libcap2_1:2.25-1 libcc1-0_7.2.0-4ubuntu1 libcilkrts5_7.2.0-4ubuntu1 libcomerr2_1.43.5-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4ubuntu1 libcurl3-gnutls_7.55.1-1ubuntu1 libdb5.3_5.3.28-13.1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu3 libdpkg-perl_1.18.24ubuntu1 libfakeroot_1.21-1ubuntu2 libfdisk1_2.30.1-0ubuntu4 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-6-dev_6.4.0-5ubuntu3 libgcc-7-dev_7.2.0-4ubuntu1 libgcc1_1:7.2.0-4ubuntu1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libglib2.0-0_2.53.6-1ubuntu2 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-6ubuntu3 libgomp1_7.2.0-4ubuntu1 libgpg-error0_1.27-3 libgsl-dev_2.4+dfsg-6 libgsl23_2.4+dfsg-6 libgslcblas0_2.4+dfsg-6 libgssapi-krb5-2_1.15.1-2 libgssapi3-heimdal_7.4.0.dfsg.1-2 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_1.5-1 libhts2_1.5-1 libhx509-5-heimdal_7.4.0.dfsg.1-2 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-3 libio-pty-perl_1:1.08-1.1build4 libip4tc0_1.6.1-2ubuntu1 libisl15_0.18-1 libitm1_7.2.0-4ubuntu1 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_24-1ubuntu2 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 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.1-0ubuntu4 libmpc3_1.0.3-1 libmpfr4_3.1.6-1 libmpx2_7.2.0-4ubuntu1 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 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-4 libperl5.24_5.24.1-2ubuntu1 libperl5.26_5.26.0-7 libpipeline1_1.4.2-1 libpng16-16_1.6.32-1 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.18.0-2 libquadmath0_7.2.0-4ubuntu1 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.4.0.dfsg.1-2 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu1 libseccomp2_2.3.1-2.1ubuntu1 libselinux1_2.6-3build2 libsemanage-common_2.6-2build2 libsemanage1_2.6-2build2 libsepol1_2.6-2 libsigsegv2_2.11-1 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.30.1-0ubuntu4 libsqlite3-0_3.19.3-3 libss2_1.43.5-1 libssl1.0.0_1.0.2g-1ubuntu13 libstdc++-6-dev_6.4.0-5ubuntu3 libstdc++-7-dev_7.2.0-4ubuntu1 libstdc++6_7.2.0-4ubuntu1 libsystemd0_234-2ubuntu10 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libubsan0_7.2.0-4ubuntu1 libudev1_234-2ubuntu10 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.30.1-0ubuntu4 libwind0-heimdal_7.4.0.dfsg.1-2 libxml2_2.9.4+dfsg1-3.1 linux-libc-dev_4.12.0-13.14 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu4 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mount_2.30.1-0ubuntu4 multiarch-support_2.26-0ubuntu1 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu13 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu4 patch_2.7.5-1build1 perl_5.26.0-7 perl-base_5.26.0-7 perl-modules-5.24_5.24.1-2ubuntu1 perl-modules-5.26_5.26.0-7 pinentry-curses_1.0.0-2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 readline-common_7.0-0ubuntu2 sbuild-build-depends-bcftools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_234-2ubuntu10 systemd-sysv_234-2ubuntu10 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tabix_1.5-1 tar_1.29b-2 tzdata_2017b-2 ubuntu-keyring_2016.10.27 util-linux_2.30.1-0ubuntu4 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sun Aug 6 00:25:26 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.4.1-3build1.dsc dpkg-source: info: extracting bcftools in bcftools-1.4.1 dpkg-source: info: unpacking bcftools_1.4.1.orig.tar.gz dpkg-source: info: unpacking bcftools_1.4.1-3build1.debian.tar.xz dpkg-source: info: applying external-libs.patch dpkg-source: info: applying compiler-flags.patch dpkg-source: info: applying destdir.patch dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying test-regidx-unsigned-char.patch dpkg-source: info: applying fix-bufffer-overflow.patch dpkg-source: info: applying fix-test_vcf_query.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-13205066 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13205066 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13205066 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.4.1-3build1 dpkg-buildpackage: info: source distribution artful dpkg-source --before-build bcftools-1.4.1 dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --parallel dh_auto_clean make -j4 distclean make[1]: Entering directory '/<>' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f gmon.out *.o *~ bcftools version.h plugins/*.so plugins/*.P rm -rf *.dSYM plugins/*.dSYM test/*.dSYM rm -f TAGS make[1]: Leaving directory '/<>' dh_autoreconf_clean dh_clean debian/rules build-arch dh build-arch --parallel dh_update_autotools_config -a -O--parallel dh_autoreconf -a -O--parallel dh_auto_configure -a -O--parallel dh_auto_build -a -O--parallel make -j4 make[1]: Entering directory '/<>' echo '#define BCFTOOLS_VERSION "1.4.1"' > version.h cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfplugin.o vcfplugin.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polysomy.o polysomy.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o peakfit.o peakfit.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/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/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/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/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/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/fixref.so version.c plugins/fixref.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/i386-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/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/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/w0ZSgG6G0P/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/w0ZSgG6G0P/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: /usr/bin/tabix /tmp/w0ZSgG6G0P/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/w0ZSgG6G0P/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/w0ZSgG6G0P/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/w0ZSgG6G0P/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/w0ZSgG6G0P/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/w0ZSgG6G0P/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/w0ZSgG6G0P/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/w0ZSgG6G0P/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/w0ZSgG6G0P/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/w0ZSgG6G0P/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/w0ZSgG6G0P/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/w0ZSgG6G0P/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/w0ZSgG6G0P/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/w0ZSgG6G0P/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/w0ZSgG6G0P/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/w0ZSgG6G0P/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/w0ZSgG6G0P/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/w0ZSgG6G0P/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/w0ZSgG6G0P/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/w0ZSgG6G0P/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/w0ZSgG6G0P/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/w0ZSgG6G0P/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/w0ZSgG6G0P/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/w0ZSgG6G0P/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/w0ZSgG6G0P/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/check.1.chk /tmp/w0ZSgG6G0P/check.2.chk /tmp/w0ZSgG6G0P/check.3.chk /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/stats.a.vcf.gz /tmp/w0ZSgG6G0P/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/w0ZSgG6G0P/stats.a.vcf.gz /tmp/w0ZSgG6G0P/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/w0ZSgG6G0P/isec.a.vcf.gz /tmp/w0ZSgG6G0P/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/w0ZSgG6G0P/isec.a.vcf.gz /tmp/w0ZSgG6G0P/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/w0ZSgG6G0P/isec.a.vcf.gz /tmp/w0ZSgG6G0P/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/w0ZSgG6G0P/isec.a.vcf.gz /tmp/w0ZSgG6G0P/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/w0ZSgG6G0P/isec.a.vcf.gz /tmp/w0ZSgG6G0P/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/w0ZSgG6G0P/isec.a.vcf.gz /tmp/w0ZSgG6G0P/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/w0ZSgG6G0P/isec.a.vcf.gz /tmp/w0ZSgG6G0P/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/w0ZSgG6G0P/isec.a.vcf.gz /tmp/w0ZSgG6G0P/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/w0ZSgG6G0P/isec.a.vcf.gz /tmp/w0ZSgG6G0P/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/w0ZSgG6G0P/isec.a.vcf.gz /tmp/w0ZSgG6G0P/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/w0ZSgG6G0P/isec.tab.gz /tmp/w0ZSgG6G0P/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/w0ZSgG6G0P/isec.tab.gz /tmp/w0ZSgG6G0P/isec.a.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/w0ZSgG6G0P/merge.a.vcf.gz /tmp/w0ZSgG6G0P/merge.b.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.a.vcf.gz /tmp/w0ZSgG6G0P/merge.b.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.a.vcf.gz /tmp/w0ZSgG6G0P/merge.b.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.a.vcf.gz /tmp/w0ZSgG6G0P/merge.b.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.a.vcf.gz /tmp/w0ZSgG6G0P/merge.b.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.a.vcf.gz /tmp/w0ZSgG6G0P/merge.b.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.2.a.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.2.a.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.2.a.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.2.a.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.2.a.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.2.a.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.3.a.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.3.a.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.4.a.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.4.a.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/gvcf.merge.1.vcf.gz /tmp/w0ZSgG6G0P/gvcf.merge.2.vcf.gz /tmp/w0ZSgG6G0P/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/w0ZSgG6G0P/gvcf.merge.1.vcf.gz /tmp/w0ZSgG6G0P/gvcf.merge.2.vcf.gz /tmp/w0ZSgG6G0P/gvcf.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/w0ZSgG6G0P/merge.gvcf.2.a.vcf.gz /tmp/w0ZSgG6G0P/merge.gvcf.2.b.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.gvcf.2.a.vcf.gz /tmp/w0ZSgG6G0P/merge.gvcf.2.b.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/merge.5.a.vcf.gz /tmp/w0ZSgG6G0P/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/w0ZSgG6G0P/merge.5.a.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/missing.vcf.gz | /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/w0ZSgG6G0P/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/w0ZSgG6G0P/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/norm.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -cx -f /<>/test/norm.fa /tmp/w0ZSgG6G0P/norm.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/w0ZSgG6G0P/norm.merge.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/norm.merge.3.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' The outputs differ: /<>/test/norm.merge.3.out /<>/test/norm.merge.3.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/norm.setref.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/norm.telomere.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/w0ZSgG6G0P/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/w0ZSgG6G0P/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/w0ZSgG6G0P/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/w0ZSgG6G0P/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/w0ZSgG6G0P/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/w0ZSgG6G0P/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/w0ZSgG6G0P/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/w0ZSgG6G0P/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/w0ZSgG6G0P/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/w0ZSgG6G0P/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/w0ZSgG6G0P/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/w0ZSgG6G0P/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/w0ZSgG6G0P/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/w0ZSgG6G0P/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/w0ZSgG6G0P/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/w0ZSgG6G0P/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/w0ZSgG6G0P/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/w0ZSgG6G0P/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/w0ZSgG6G0P/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/w0ZSgG6G0P/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/w0ZSgG6G0P/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/w0ZSgG6G0P/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/w0ZSgG6G0P/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/w0ZSgG6G0P/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/w0ZSgG6G0P/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/w0ZSgG6G0P/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/w0ZSgG6G0P/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/w0ZSgG6G0P/view.vectors.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[2]="C"' /tmp/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[4]="EE"' /tmp/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[1]="BB"' /tmp/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/w0ZSgG6G0P/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/w0ZSgG6G0P/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/w0ZSgG6G0P/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/w0ZSgG6G0P/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/w0ZSgG6G0P/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/w0ZSgG6G0P/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/w0ZSgG6G0P/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/w0ZSgG6G0P/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w0ZSgG6G0P/regions.tab.gz /tmp/w0ZSgG6G0P/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w0ZSgG6G0P/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/w0ZSgG6G0P/regions.tab.gz /tmp/w0ZSgG6G0P/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w0ZSgG6G0P/regions.bed /tmp/w0ZSgG6G0P/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w0ZSgG6G0P/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/w0ZSgG6G0P/regions.bed /tmp/w0ZSgG6G0P/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w0ZSgG6G0P/regions.bed.gz /tmp/w0ZSgG6G0P/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w0ZSgG6G0P/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/w0ZSgG6G0P/regions.bed.gz /tmp/w0ZSgG6G0P/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/w0ZSgG6G0P/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/w0ZSgG6G0P/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/w0ZSgG6G0P/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/w0ZSgG6G0P/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/w0ZSgG6G0P/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/w0ZSgG6G0P/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/annots4.vcf.gz -c +INFO /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/annots4.vcf.gz -c +INFO /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/w0ZSgG6G0P/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/w0ZSgG6G0P/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/w0ZSgG6G0P/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/w0ZSgG6G0P/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/w0ZSgG6G0P/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/w0ZSgG6G0P/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/w0ZSgG6G0P/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/concat.1.a.vcf.gz /tmp/w0ZSgG6G0P/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/w0ZSgG6G0P/concat.1.a.vcf.gz /tmp/w0ZSgG6G0P/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/w0ZSgG6G0P/concat.1.a.bcf /tmp/w0ZSgG6G0P/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/w0ZSgG6G0P/concat.1.a.bcf /tmp/w0ZSgG6G0P/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/w0ZSgG6G0P/concat.2.a.vcf.gz /tmp/w0ZSgG6G0P/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/w0ZSgG6G0P/concat.2.a.vcf.gz /tmp/w0ZSgG6G0P/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/w0ZSgG6G0P/concat.2.a.bcf /tmp/w0ZSgG6G0P/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/w0ZSgG6G0P/concat.2.a.bcf /tmp/w0ZSgG6G0P/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/w0ZSgG6G0P/concat.2.a.vcf.gz /tmp/w0ZSgG6G0P/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/w0ZSgG6G0P/concat.2.a.vcf.gz /tmp/w0ZSgG6G0P/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/w0ZSgG6G0P/concat.2.a.bcf /tmp/w0ZSgG6G0P/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/w0ZSgG6G0P/concat.2.a.bcf /tmp/w0ZSgG6G0P/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/w0ZSgG6G0P/concat.3.a.vcf.gz /tmp/w0ZSgG6G0P/concat.3.b.vcf.gz /tmp/w0ZSgG6G0P/concat.3.0.vcf.gz /tmp/w0ZSgG6G0P/concat.3.c.vcf.gz /tmp/w0ZSgG6G0P/concat.3.d.vcf.gz /tmp/w0ZSgG6G0P/concat.3.e.vcf.gz /tmp/w0ZSgG6G0P/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/w0ZSgG6G0P/concat.3.a.vcf.gz /tmp/w0ZSgG6G0P/concat.3.b.vcf.gz /tmp/w0ZSgG6G0P/concat.3.0.vcf.gz /tmp/w0ZSgG6G0P/concat.3.c.vcf.gz /tmp/w0ZSgG6G0P/concat.3.d.vcf.gz /tmp/w0ZSgG6G0P/concat.3.e.vcf.gz /tmp/w0ZSgG6G0P/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/w0ZSgG6G0P/concat.3.a.bcf /tmp/w0ZSgG6G0P/concat.3.b.bcf /tmp/w0ZSgG6G0P/concat.3.0.bcf /tmp/w0ZSgG6G0P/concat.3.c.bcf /tmp/w0ZSgG6G0P/concat.3.d.bcf /tmp/w0ZSgG6G0P/concat.3.e.bcf /tmp/w0ZSgG6G0P/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/w0ZSgG6G0P/concat.3.a.bcf /tmp/w0ZSgG6G0P/concat.3.b.bcf /tmp/w0ZSgG6G0P/concat.3.0.bcf /tmp/w0ZSgG6G0P/concat.3.c.bcf /tmp/w0ZSgG6G0P/concat.3.d.bcf /tmp/w0ZSgG6G0P/concat.3.e.bcf /tmp/w0ZSgG6G0P/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1892148577 .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/w0ZSgG6G0P/naive_concat.0.bcf /tmp/w0ZSgG6G0P/naive_concat.1.bcf /tmp/w0ZSgG6G0P/naive_concat.2.bcf /tmp/w0ZSgG6G0P/naive_concat.3.bcf /tmp/w0ZSgG6G0P/naive_concat.4.bcf /tmp/w0ZSgG6G0P/naive_concat.5.bcf /tmp/w0ZSgG6G0P/naive_concat.6.bcf /tmp/w0ZSgG6G0P/naive_concat.7.bcf /tmp/w0ZSgG6G0P/naive_concat.8.bcf /tmp/w0ZSgG6G0P/naive_concat.9.bcf | /<>/bcftools view -H .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/w0ZSgG6G0P/naive_concat.0.vcf.gz /tmp/w0ZSgG6G0P/naive_concat.1.vcf.gz /tmp/w0ZSgG6G0P/naive_concat.2.vcf.gz /tmp/w0ZSgG6G0P/naive_concat.3.vcf.gz /tmp/w0ZSgG6G0P/naive_concat.4.vcf.gz /tmp/w0ZSgG6G0P/naive_concat.5.vcf.gz /tmp/w0ZSgG6G0P/naive_concat.6.vcf.gz /tmp/w0ZSgG6G0P/naive_concat.7.vcf.gz /tmp/w0ZSgG6G0P/naive_concat.8.vcf.gz /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w0ZSgG6G0P/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/w0ZSgG6G0P/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w0ZSgG6G0P/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/w0ZSgG6G0P/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w0ZSgG6G0P/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/w0ZSgG6G0P/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w0ZSgG6G0P/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/w0ZSgG6G0P/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w0ZSgG6G0P/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/w0ZSgG6G0P/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w0ZSgG6G0P/empty.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/w0ZSgG6G0P/rename.map -Ov /tmp/w0ZSgG6G0P/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/w0ZSgG6G0P/rename.map -Ob /tmp/w0ZSgG6G0P/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/w0ZSgG6G0P/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/w0ZSgG6G0P/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/w0ZSgG6G0P/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/convert.vcf.gz | /<>/bcftools convert -g -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/w0ZSgG6G0P/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/convert.vcf.gz | /<>/bcftools convert -g .,- 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/w0ZSgG6G0P/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/w0ZSgG6G0P/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/w0ZSgG6G0P/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/w0ZSgG6G0P/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/w0ZSgG6G0P/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/check.vcf.gz | /<>/bcftools convert -g -,. --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/w0ZSgG6G0P/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/check.vcf.gz | /<>/bcftools convert -g .,- --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/w0ZSgG6G0P/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/w0ZSgG6G0P/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/w0ZSgG6G0P/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/convert.vcf.gz | /<>/bcftools convert -h -,.,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/w0ZSgG6G0P/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/convert.vcf.gz | /<>/bcftools convert -h .,-,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/w0ZSgG6G0P/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/convert.vcf.gz | /<>/bcftools convert --hapsample -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/w0ZSgG6G0P/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/convert.vcf.gz | /<>/bcftools convert --hapsample .,- 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools convert --no-version --gvcf2vcf -f /<>/test/gvcf.fa /tmp/w0ZSgG6G0P/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/w0ZSgG6G0P/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/w0ZSgG6G0P/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/w0ZSgG6G0P/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/w0ZSgG6G0P/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/w0ZSgG6G0P/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/w0ZSgG6G0P/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/w0ZSgG6G0P/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/w0ZSgG6G0P/consensus.vcf.gz -f /<>/test/consensus.fa -i -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/w0ZSgG6G0P/consensus.vcf.gz -f /<>/test/consensus.fa -i -m /<>/test/consensus.tab -c /tmp/w0ZSgG6G0P/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/w0ZSgG6G0P/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/w0ZSgG6G0P/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/w0ZSgG6G0P/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/w0ZSgG6G0P/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/w0ZSgG6G0P/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/w0ZSgG6G0P/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/w0ZSgG6G0P/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/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/w0ZSgG6G0P/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/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/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/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-donor2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/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/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-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/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/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-donor3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/ENST00000256452/ENST00000256452.fa -g /<>/test/csq/ENST00000256452/ENST00000256452.gff /<>/test/csq/ENST00000256452/intron.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000256452/ENST00000256452.gff ... Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/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/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/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/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/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/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/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/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 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 20170909-0943 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 20696 Build-Time: 74 Distribution: artful-proposed Fail-Stage: build Host Architecture: i386 Install-Time: 14 Job: bcftools_1.4.1-3build1.dsc Machine Architecture: amd64 Package: bcftools Package-Time: 90 Source-Version: 1.4.1-3build1 Space: 20696 Status: attempted Version: 1.4.1-3build1 -------------------------------------------------------------------------------- Finished at 20170909-0943 Build needed 00:01:30, 20696k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13205066 Scanning for processes to kill in build PACKAGEBUILD-13205066 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13205066 Stopping target for build PACKAGEBUILD-13205066 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-13205066 Removing build PACKAGEBUILD-13205066