https://launchpad.net/ubuntu/+source/bcftools/1.9-1/+build/15625499 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-019 4.4.0-145-generic #171-Ubuntu SMP Tue Mar 26 12:43:03 UTC 2019 s390x Buildd toolchain package versions: launchpad-buildd_169 python-lpbuildd_169 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_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 9 Apr 05:30:58 ntpdate[1800]: adjust time server 10.211.37.1 offset 0.472776 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=disco --arch=s390x PACKAGEBUILD-15625499 --image-type chroot /home/buildd/filecache-default/5f92d5ecab7ce0d953bb2def2bd7e5fe5fb7c904 Creating target for build PACKAGEBUILD-15625499 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=disco --arch=s390x PACKAGEBUILD-15625499 Starting target for build PACKAGEBUILD-15625499 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=disco --arch=s390x PACKAGEBUILD-15625499 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15625499 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=disco --arch=s390x PACKAGEBUILD-15625499 Updating target for build PACKAGEBUILD-15625499 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [256 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [66.2 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [66.2 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [107 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main s390x Packages [940 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe s390x Packages [8709 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5261 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main s390x Packages [24.2 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [13.8 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe s390x Packages [98.8 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [64.5 kB] Fetched 16.1 MB in 4s (3975 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libreadline7 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: gcc-9-base libreadline8 The following packages will be upgraded: adduser apt base-passwd bash binutils binutils-common binutils-s390x-linux-gnu bsdutils build-essential ca-certificates coreutils cpp cpp-8 dash debconf debianutils diffutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk findutils g++ g++-8 gcc gcc-8 gcc-8-base gpg gpg-agent gpgconf gpgv grep gzip init init-system-helpers libacl1 libapparmor1 libapt-pkg5.0 libargon2-1 libasan5 libassuan0 libatomic1 libattr1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcomerr2 libcryptsetup12 libdb5.3 libdebconfclient0 libdpkg-perl libext2fs2 libfdisk1 libgcc-8-dev libgcc1 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libhogweed4 libidn11 libitm1 libjson-c3 libkmod2 liblz4-1 liblzma5 libmount1 libmpfr6 libncurses6 libncursesw6 libnettle6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre3 libperl5.28 libpng16-16 libprocps7 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-8-dev libstdc++6 libsystemd0 libtinfo6 libubsan1 libudev1 libunistring2 libuuid1 libzstd1 linux-libc-dev login lsb-base mount multiarch-support ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.28 pkgbinarymangler procps readline-common sed systemd systemd-sysv tar tzdata util-linux xz-utils zlib1g 128 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 64.8 MB of archives. After this operation, 10.4 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main s390x debianutils s390x 4.8.6.1 [85.0 kB] Get:2 http://ftpmaster.internal/ubuntu disco/main s390x bash s390x 5.0-3ubuntu1 [602 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main s390x bsdutils s390x 1:2.33.1-0.1ubuntu2 [61.2 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main s390x coreutils s390x 8.30-1ubuntu1 [1216 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main s390x lsb-base all 10.2019031300ubuntu1 [12.5 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main s390x tar s390x 1.30+dfsg-5 [230 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main s390x dpkg s390x 1.19.6ubuntu1 [1110 kB] Get:8 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libc6-dev s390x 2.29-0ubuntu2 [2033 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libc-dev-bin s390x 2.29-0ubuntu2 [62.1 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main s390x linux-libc-dev s390x 5.0.0-8.9 [1031 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libc6 s390x 2.29-0ubuntu2 [2249 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libc-bin s390x 2.29-0ubuntu2 [513 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main s390x gcc-9-base s390x 9-20190402-1ubuntu1 [17.0 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main s390x libgcc1 s390x 1:9-20190402-1ubuntu1 [24.4 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main s390x libperl5.28 s390x 5.28.1-6 [3669 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main s390x perl s390x 5.28.1-6 [204 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main s390x perl-base s390x 5.28.1-6 [1420 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main s390x perl-modules-5.28 all 5.28.1-6 [2818 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main s390x libdb5.3 s390x 5.3.28+dfsg1-0.5 [608 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main s390x libgdbm6 s390x 1.18.1-4 [26.8 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main s390x libgdbm-compat4 s390x 1.18.1-4 [6260 B] Get:22 http://ftpmaster.internal/ubuntu disco/main s390x zlib1g s390x 1:1.2.11.dfsg-1ubuntu2 [51.8 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main s390x debconf all 1.5.71 [122 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main s390x dash s390x 0.5.10.2-4ubuntu1 [83.6 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main s390x diffutils s390x 1:3.7-2 [193 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main s390x findutils s390x 4.6.0+git+20190209-2 [321 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main s390x grep s390x 3.3-1 [146 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main s390x gzip s390x 1.9-3 [92.7 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main s390x libsmartcols1 s390x 2.33.1-0.1ubuntu2 [85.8 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main s390x libuuid1 s390x 2.33.1-0.1ubuntu2 [21.0 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main s390x libblkid1 s390x 2.33.1-0.1ubuntu2 [123 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main s390x libfdisk1 s390x 2.33.1-0.1ubuntu2 [159 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main s390x libmount1 s390x 2.33.1-0.1ubuntu2 [133 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main s390x libncurses6 s390x 6.1+20181013-2ubuntu2 [94.4 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main s390x libtinfo6 s390x 6.1+20181013-2ubuntu2 [80.2 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main s390x libncursesw6 s390x 6.1+20181013-2ubuntu2 [120 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main s390x fdisk s390x 2.33.1-0.1ubuntu2 [111 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main s390x login s390x 1:4.5-1.1ubuntu2 [262 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main s390x util-linux s390x 2.33.1-0.1ubuntu2 [960 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main s390x ncurses-bin s390x 6.1+20181013-2ubuntu2 [160 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main s390x sed s390x 4.7-1 [187 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main s390x libdebconfclient0 s390x 0.247ubuntu1 [6232 B] Get:43 http://ftpmaster.internal/ubuntu disco/main s390x base-passwd s390x 3.5.46 [46.3 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main s390x init-system-helpers all 1.56+nmu1 [38.2 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main s390x ncurses-base all 6.1+20181013-2ubuntu2 [17.9 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main s390x libnettle6 s390x 3.4.1-1 [121 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main s390x libhogweed4 s390x 3.4.1-1 [138 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main s390x libp11-kit0 s390x 0.23.15-2 [184 kB] Get:49 http://ftpmaster.internal/ubuntu disco/main s390x libunistring2 s390x 0.9.10-1ubuntu2 [359 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main s390x libgnutls30 s390x 3.6.5-2ubuntu1 [661 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main s390x liblz4-1 s390x 1.8.3-1ubuntu1 [56.1 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main s390x liblzma5 s390x 5.2.4-1 [91.5 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main s390x libstdc++6 s390x 9-20190402-1ubuntu1 [494 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main s390x libudev1 s390x 240-6ubuntu3 [58.1 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main s390x libzstd1 s390x 1.3.8+dfsg-3 [204 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main s390x libapt-pkg5.0 s390x 1.8.0 [750 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main s390x libpam0g s390x 1.3.1-5ubuntu1 [53.9 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main s390x libsemanage-common all 2.8-2 [7016 B] Get:59 http://ftpmaster.internal/ubuntu disco/main s390x libsemanage1 s390x 2.8-2 [78.5 kB] Get:60 http://ftpmaster.internal/ubuntu disco/main s390x libpam-modules-bin s390x 1.3.1-5ubuntu1 [35.8 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main s390x libpam-modules s390x 1.3.1-5ubuntu1 [238 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main s390x passwd s390x 1:4.5-1.1ubuntu2 [797 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main s390x adduser all 3.118ubuntu1 [163 kB] Get:64 http://ftpmaster.internal/ubuntu disco/main s390x libgpg-error0 s390x 1.35-1 [53.9 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main s390x gpgv s390x 2.2.12-1ubuntu3 [180 kB] Get:66 http://ftpmaster.internal/ubuntu disco/main s390x apt s390x 1.8.0 [1167 kB] Get:67 http://ftpmaster.internal/ubuntu disco/main s390x systemd-sysv s390x 240-6ubuntu3 [9376 B] Get:68 http://ftpmaster.internal/ubuntu disco/main s390x libacl1 s390x 2.2.53-4 [17.9 kB] Get:69 http://ftpmaster.internal/ubuntu disco/main s390x libapparmor1 s390x 2.13.2-9ubuntu5 [33.2 kB] Get:70 http://ftpmaster.internal/ubuntu disco/main s390x libcap2 s390x 1:2.25-2 [13.3 kB] Get:71 http://ftpmaster.internal/ubuntu disco/main s390x libargon2-1 s390x 0~20171227-0.2 [35.7 kB] Get:72 http://ftpmaster.internal/ubuntu disco/main s390x libjson-c3 s390x 0.12.1+ds-2 [21.4 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main s390x libssl1.1 s390x 1.1.1b-1ubuntu2 [964 kB] Get:74 http://ftpmaster.internal/ubuntu disco/main s390x libcryptsetup12 s390x 2:2.1.0-1ubuntu1 [131 kB] Get:75 http://ftpmaster.internal/ubuntu disco/main s390x libidn11 s390x 1.33-2.2ubuntu2 [44.6 kB] Get:76 http://ftpmaster.internal/ubuntu disco/main s390x libkmod2 s390x 25-1ubuntu3 [37.9 kB] Get:77 http://ftpmaster.internal/ubuntu disco/main s390x mount s390x 2.33.1-0.1ubuntu2 [108 kB] Get:78 http://ftpmaster.internal/ubuntu disco/main s390x systemd s390x 240-6ubuntu3 [2990 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main s390x libsystemd0 s390x 240-6ubuntu3 [219 kB] Get:80 http://ftpmaster.internal/ubuntu disco/main s390x libext2fs2 s390x 1.44.6-1 [155 kB] Get:81 http://ftpmaster.internal/ubuntu disco/main s390x e2fsprogs s390x 1.44.6-1 [492 kB] Get:82 http://ftpmaster.internal/ubuntu disco/main s390x init s390x 1.56+nmu1 [6080 B] Get:83 http://ftpmaster.internal/ubuntu disco/main s390x libattr1 s390x 1:2.4.48-4 [12.0 kB] Get:84 http://ftpmaster.internal/ubuntu disco/main s390x libcap-ng0 s390x 0.7.9-2 [10.6 kB] Get:85 http://ftpmaster.internal/ubuntu disco/main s390x libpam-runtime all 1.3.1-5ubuntu1 [37.3 kB] Get:86 http://ftpmaster.internal/ubuntu disco/main s390x libpcre3 s390x 2:8.39-12 [154 kB] Get:87 http://ftpmaster.internal/ubuntu disco/main s390x libcom-err2 s390x 1.44.6-1 [9416 B] Get:88 http://ftpmaster.internal/ubuntu disco/main s390x libprocps7 s390x 2:3.3.15-2ubuntu2 [30.9 kB] Get:89 http://ftpmaster.internal/ubuntu disco/main s390x libss2 s390x 1.44.6-1 [10.6 kB] Get:90 http://ftpmaster.internal/ubuntu disco/main s390x procps s390x 2:3.3.15-2ubuntu2 [220 kB] Get:91 http://ftpmaster.internal/ubuntu disco/main s390x openssl s390x 1.1.1b-1ubuntu2 [604 kB] Get:92 http://ftpmaster.internal/ubuntu disco/main s390x ca-certificates all 20190110 [146 kB] Get:93 http://ftpmaster.internal/ubuntu disco/main s390x readline-common all 8.0-1 [53.4 kB] Get:94 http://ftpmaster.internal/ubuntu disco/main s390x libreadline8 s390x 8.0-1 [122 kB] Get:95 http://ftpmaster.internal/ubuntu disco/main s390x libsqlite3-0 s390x 3.27.2-2 [496 kB] Get:96 http://ftpmaster.internal/ubuntu disco/main s390x tzdata all 2019a-1 [187 kB] Get:97 http://ftpmaster.internal/ubuntu disco/main s390x xz-utils s390x 5.2.4-1 [80.3 kB] Get:98 http://ftpmaster.internal/ubuntu disco/main s390x libpng16-16 s390x 1.6.36-5 [173 kB] Get:99 http://ftpmaster.internal/ubuntu disco-proposed/main s390x multiarch-support s390x 2.29-0ubuntu2 [6916 B] Get:100 http://ftpmaster.internal/ubuntu disco/main s390x binutils-s390x-linux-gnu s390x 2.32-7ubuntu4 [1690 kB] Get:101 http://ftpmaster.internal/ubuntu disco/main s390x libbinutils s390x 2.32-7ubuntu4 [296 kB] Get:102 http://ftpmaster.internal/ubuntu disco/main s390x binutils s390x 2.32-7ubuntu4 [3316 B] Get:103 http://ftpmaster.internal/ubuntu disco/main s390x binutils-common s390x 2.32-7ubuntu4 [200 kB] Get:104 http://ftpmaster.internal/ubuntu disco/main s390x libubsan1 s390x 9-20190402-1ubuntu1 [123 kB] Get:105 http://ftpmaster.internal/ubuntu disco/main s390x libgomp1 s390x 9-20190402-1ubuntu1 [81.8 kB] Get:106 http://ftpmaster.internal/ubuntu disco/main s390x libitm1 s390x 9-20190402-1ubuntu1 [26.8 kB] Get:107 http://ftpmaster.internal/ubuntu disco/main s390x libatomic1 s390x 9-20190402-1ubuntu1 [8376 B] Get:108 http://ftpmaster.internal/ubuntu disco/main s390x libasan5 s390x 9-20190402-1ubuntu1 [350 kB] Get:109 http://ftpmaster.internal/ubuntu disco-proposed/main s390x g++-8 s390x 8.3.0-6ubuntu1 [7954 kB] Get:110 http://ftpmaster.internal/ubuntu disco-proposed/main s390x gcc-8 s390x 8.3.0-6ubuntu1 [7716 kB] Get:111 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libstdc++-8-dev s390x 8.3.0-6ubuntu1 [1514 kB] Get:112 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libgcc-8-dev s390x 8.3.0-6ubuntu1 [651 kB] Get:113 http://ftpmaster.internal/ubuntu disco/main s390x libcc1-0 s390x 9-20190402-1ubuntu1 [45.1 kB] Get:114 http://ftpmaster.internal/ubuntu disco-proposed/main s390x cpp-8 s390x 8.3.0-6ubuntu1 [6883 kB] Get:115 http://ftpmaster.internal/ubuntu disco-proposed/main s390x gcc-8-base s390x 8.3.0-6ubuntu1 [18.6 kB] Get:116 http://ftpmaster.internal/ubuntu disco/main s390x libmpfr6 s390x 4.0.2-1 [229 kB] Get:117 http://ftpmaster.internal/ubuntu disco/main s390x g++ s390x 4:8.3.0-1ubuntu3 [1596 B] Get:118 http://ftpmaster.internal/ubuntu disco/main s390x gcc s390x 4:8.3.0-1ubuntu3 [5204 B] Get:119 http://ftpmaster.internal/ubuntu disco/main s390x cpp s390x 4:8.3.0-1ubuntu3 [27.6 kB] Get:120 http://ftpmaster.internal/ubuntu disco/main s390x dpkg-dev all 1.19.6ubuntu1 [675 kB] Get:121 http://ftpmaster.internal/ubuntu disco/main s390x libdpkg-perl all 1.19.6ubuntu1 [230 kB] Get:122 http://ftpmaster.internal/ubuntu disco/main s390x build-essential s390x 12.6ubuntu1 [4664 B] Get:123 http://ftpmaster.internal/ubuntu disco/main s390x e2fslibs s390x 1.44.6-1 [2700 B] Get:124 http://ftpmaster.internal/ubuntu disco/main s390x libassuan0 s390x 2.5.2-1 [32.1 kB] Get:125 http://ftpmaster.internal/ubuntu disco/main s390x gpg s390x 2.2.12-1ubuntu3 [431 kB] Get:126 http://ftpmaster.internal/ubuntu disco/main s390x gpgconf s390x 2.2.12-1ubuntu3 [115 kB] Get:127 http://ftpmaster.internal/ubuntu disco/main s390x gpg-agent s390x 2.2.12-1ubuntu3 [209 kB] Get:128 http://ftpmaster.internal/ubuntu disco/main s390x libcomerr2 s390x 1.44.6-1 [2692 B] Get:129 http://ftpmaster.internal/ubuntu disco/main s390x optipng s390x 0.7.7-1 [82.0 kB] Get:130 http://ftpmaster.internal/ubuntu disco/main s390x pkgbinarymangler all 144 [55.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 64.8 MB in 1s (75.7 MB/s) (Reading database ... 12438 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6.1_s390x.deb ... Unpacking debianutils (4.8.6.1) over (4.8.6) ... Setting up debianutils (4.8.6.1) ... (Reading database ... 12438 files and directories currently installed.) Preparing to unpack .../bash_5.0-3ubuntu1_s390x.deb ... Unpacking bash (5.0-3ubuntu1) over (4.4.18-2ubuntu3) ... Setting up bash (5.0-3ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12438 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.33.1-0.1ubuntu2_s390x.deb ... Unpacking bsdutils (1:2.33.1-0.1ubuntu2) over (1:2.32-0.1ubuntu2) ... Setting up bsdutils (1:2.33.1-0.1ubuntu2) ... (Reading database ... 12438 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-1ubuntu1_s390x.deb ... Unpacking coreutils (8.30-1ubuntu1) over (8.28-1ubuntu2) ... Setting up coreutils (8.30-1ubuntu1) ... (Reading database ... 12438 files and directories currently installed.) Preparing to unpack .../lsb-base_10.2019031300ubuntu1_all.deb ... Unpacking lsb-base (10.2019031300ubuntu1) over (9.20170808ubuntu1) ... Preparing to unpack .../tar_1.30+dfsg-5_s390x.deb ... Unpacking tar (1.30+dfsg-5) over (1.30+dfsg-3) ... Setting up tar (1.30+dfsg-5) ... (Reading database ... 12437 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.6ubuntu1_s390x.deb ... Unpacking dpkg (1.19.6ubuntu1) over (1.19.2ubuntu1) ... Setting up dpkg (1.19.6ubuntu1) ... Installing new version of config file /etc/cron.daily/dpkg ... (Reading database ... 12445 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.29-0ubuntu2_s390x.deb ... Unpacking libc6-dev:s390x (2.29-0ubuntu2) over (2.28-0ubuntu1) ... Preparing to unpack .../libc-dev-bin_2.29-0ubuntu2_s390x.deb ... Unpacking libc-dev-bin (2.29-0ubuntu2) over (2.28-0ubuntu1) ... Preparing to unpack .../linux-libc-dev_5.0.0-8.9_s390x.deb ... Unpacking linux-libc-dev:s390x (5.0.0-8.9) over (4.18.0-11.12) ... Preparing to unpack .../libc6_2.29-0ubuntu2_s390x.deb ... Unpacking libc6:s390x (2.29-0ubuntu2) over (2.28-0ubuntu1) ... Setting up libc6:s390x (2.29-0ubuntu2) ... (Reading database ... 12473 files and directories currently installed.) Preparing to unpack .../libc-bin_2.29-0ubuntu2_s390x.deb ... Unpacking libc-bin (2.29-0ubuntu2) over (2.28-0ubuntu1) ... Setting up libc-bin (2.29-0ubuntu2) ... Selecting previously unselected package gcc-9-base:s390x. (Reading database ... 12473 files and directories currently installed.) Preparing to unpack .../gcc-9-base_9-20190402-1ubuntu1_s390x.deb ... Unpacking gcc-9-base:s390x (9-20190402-1ubuntu1) ... Setting up gcc-9-base:s390x (9-20190402-1ubuntu1) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a9-20190402-1ubuntu1_s390x.deb ... Unpacking libgcc1:s390x (1:9-20190402-1ubuntu1) over (1:8.2.0-12ubuntu1) ... Setting up libgcc1:s390x (1:9-20190402-1ubuntu1) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../libperl5.28_5.28.1-6_s390x.deb ... Unpacking libperl5.28:s390x (5.28.1-6) over (5.28.1-3) ... Preparing to unpack .../perl_5.28.1-6_s390x.deb ... Unpacking perl (5.28.1-6) over (5.28.1-3) ... Preparing to unpack .../perl-base_5.28.1-6_s390x.deb ... Unpacking perl-base (5.28.1-6) over (5.28.1-3) ... Setting up perl-base (5.28.1-6) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../perl-modules-5.28_5.28.1-6_all.deb ... Unpacking perl-modules-5.28 (5.28.1-6) over (5.28.1-3) ... Preparing to unpack .../libdb5.3_5.3.28+dfsg1-0.5_s390x.deb ... Unpacking libdb5.3:s390x (5.3.28+dfsg1-0.5) over (5.3.28+dfsg1-0.2) ... Setting up libdb5.3:s390x (5.3.28+dfsg1-0.5) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../libgdbm6_1.18.1-4_s390x.deb ... Unpacking libgdbm6:s390x (1.18.1-4) over (1.18.1-2) ... Preparing to unpack .../libgdbm-compat4_1.18.1-4_s390x.deb ... Unpacking libgdbm-compat4:s390x (1.18.1-4) over (1.18.1-2) ... Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-1ubuntu2_s390x.deb ... Unpacking zlib1g:s390x (1:1.2.11.dfsg-1ubuntu2) over (1:1.2.11.dfsg-0ubuntu2) ... Setting up zlib1g:s390x (1:1.2.11.dfsg-1ubuntu2) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../debconf_1.5.71_all.deb ... Unpacking debconf (1.5.71) over (1.5.69) ... Setting up debconf (1.5.71) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-4ubuntu1_s390x.deb ... Unpacking dash (0.5.10.2-4ubuntu1) over (0.5.10.2-2) ... Setting up dash (0.5.10.2-4ubuntu1) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.7-2_s390x.deb ... Unpacking diffutils (1:3.7-2) over (1:3.6-1) ... Setting up diffutils (1:3.7-2) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../findutils_4.6.0+git+20190209-2_s390x.deb ... Unpacking findutils (4.6.0+git+20190209-2) over (4.6.0+git+20181018-1) ... Setting up findutils (4.6.0+git+20190209-2) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../archives/grep_3.3-1_s390x.deb ... Unpacking grep (3.3-1) over (3.1-3) ... Setting up grep (3.3-1) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../archives/gzip_1.9-3_s390x.deb ... Unpacking gzip (1.9-3) over (1.6-5ubuntu2) ... Setting up gzip (1.9-3) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.33.1-0.1ubuntu2_s390x.deb ... Unpacking libsmartcols1:s390x (2.33.1-0.1ubuntu2) over (2.32-0.1ubuntu2) ... Setting up libsmartcols1:s390x (2.33.1-0.1ubuntu2) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../libuuid1_2.33.1-0.1ubuntu2_s390x.deb ... Unpacking libuuid1:s390x (2.33.1-0.1ubuntu2) over (2.32-0.1ubuntu2) ... Setting up libuuid1:s390x (2.33.1-0.1ubuntu2) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../libblkid1_2.33.1-0.1ubuntu2_s390x.deb ... Unpacking libblkid1:s390x (2.33.1-0.1ubuntu2) over (2.32-0.1ubuntu2) ... Setting up libblkid1:s390x (2.33.1-0.1ubuntu2) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../libfdisk1_2.33.1-0.1ubuntu2_s390x.deb ... Unpacking libfdisk1:s390x (2.33.1-0.1ubuntu2) over (2.32-0.1ubuntu2) ... Setting up libfdisk1:s390x (2.33.1-0.1ubuntu2) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../libmount1_2.33.1-0.1ubuntu2_s390x.deb ... Unpacking libmount1:s390x (2.33.1-0.1ubuntu2) over (2.32-0.1ubuntu2) ... Setting up libmount1:s390x (2.33.1-0.1ubuntu2) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../libncurses6_6.1+20181013-2ubuntu2_s390x.deb ... Unpacking libncurses6:s390x (6.1+20181013-2ubuntu2) over (6.1+20180210-4ubuntu1) ... Preparing to unpack .../libtinfo6_6.1+20181013-2ubuntu2_s390x.deb ... Unpacking libtinfo6:s390x (6.1+20181013-2ubuntu2) over (6.1+20180210-4ubuntu1) ... Setting up libtinfo6:s390x (6.1+20181013-2ubuntu2) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.1+20181013-2ubuntu2_s390x.deb ... Unpacking libncursesw6:s390x (6.1+20181013-2ubuntu2) over (6.1+20180210-4ubuntu1) ... Setting up libncursesw6:s390x (6.1+20181013-2ubuntu2) ... (Reading database ... 12479 files and directories currently installed.) Preparing to unpack .../fdisk_2.33.1-0.1ubuntu2_s390x.deb ... Unpacking fdisk (2.33.1-0.1ubuntu2) over (2.32-0.1ubuntu2) ... Setting up fdisk (2.33.1-0.1ubuntu2) ... (Reading database ... 12482 files and directories currently installed.) Preparing to unpack .../util-linux_2.33.1-0.1ubuntu2_s390x.deb ... Unpacking util-linux (2.33.1-0.1ubuntu2) over (2.32-0.1ubuntu2) ... Replacing files in old package login (1:4.5-1ubuntu1) ... Preparing to unpack .../login_1%3a4.5-1.1ubuntu2_s390x.deb ... Unpacking login (1:4.5-1.1ubuntu2) over (1:4.5-1ubuntu1) ... Setting up login (1:4.5-1.1ubuntu2) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.1+20181013-2ubuntu2_s390x.deb ... Unpacking ncurses-bin (6.1+20181013-2ubuntu2) over (6.1+20180210-4ubuntu1) ... Setting up ncurses-bin (6.1+20181013-2ubuntu2) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../archives/sed_4.7-1_s390x.deb ... Unpacking sed (4.7-1) over (4.5-2) ... Setting up sed (4.7-1) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.247ubuntu1_s390x.deb ... Unpacking libdebconfclient0:s390x (0.247ubuntu1) over (0.244ubuntu1) ... Setting up libdebconfclient0:s390x (0.247ubuntu1) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../base-passwd_3.5.46_s390x.deb ... Unpacking base-passwd (3.5.46) over (3.5.45) ... Setting up base-passwd (3.5.46) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.56+nmu1_all.deb ... Unpacking init-system-helpers (1.56+nmu1) over (1.56) ... Setting up init-system-helpers (1.56+nmu1) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.1+20181013-2ubuntu2_all.deb ... Unpacking ncurses-base (6.1+20181013-2ubuntu2) over (6.1+20180210-4ubuntu1) ... Setting up ncurses-base (6.1+20181013-2ubuntu2) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libnettle6_3.4.1-1_s390x.deb ... Unpacking libnettle6:s390x (3.4.1-1) over (3.4.1~rc1-1) ... Setting up libnettle6:s390x (3.4.1-1) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libhogweed4_3.4.1-1_s390x.deb ... Unpacking libhogweed4:s390x (3.4.1-1) over (3.4.1~rc1-1) ... Setting up libhogweed4:s390x (3.4.1-1) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.23.15-2_s390x.deb ... Unpacking libp11-kit0:s390x (0.23.15-2) over (0.23.14-2) ... Setting up libp11-kit0:s390x (0.23.15-2) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libunistring2_0.9.10-1ubuntu2_s390x.deb ... Unpacking libunistring2:s390x (0.9.10-1ubuntu2) over (0.9.10-1ubuntu1) ... Setting up libunistring2:s390x (0.9.10-1ubuntu2) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.5-2ubuntu1_s390x.deb ... Unpacking libgnutls30:s390x (3.6.5-2ubuntu1) over (3.6.4-2ubuntu2) ... Setting up libgnutls30:s390x (3.6.5-2ubuntu1) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.8.3-1ubuntu1_s390x.deb ... Unpacking liblz4-1:s390x (1.8.3-1ubuntu1) over (1.8.2-1ubuntu1) ... Setting up liblz4-1:s390x (1.8.3-1ubuntu1) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.4-1_s390x.deb ... Unpacking liblzma5:s390x (5.2.4-1) over (5.2.2-1.3) ... Setting up liblzma5:s390x (5.2.4-1) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libstdc++6_9-20190402-1ubuntu1_s390x.deb ... Unpacking libstdc++6:s390x (9-20190402-1ubuntu1) over (8.2.0-12ubuntu1) ... Setting up libstdc++6:s390x (9-20190402-1ubuntu1) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libudev1_240-6ubuntu3_s390x.deb ... Unpacking libudev1:s390x (240-6ubuntu3) over (239-7ubuntu15) ... Setting up libudev1:s390x (240-6ubuntu3) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libzstd1_1.3.8+dfsg-3_s390x.deb ... Unpacking libzstd1:s390x (1.3.8+dfsg-3) over (1.3.5+dfsg-1ubuntu1) ... Setting up libzstd1:s390x (1.3.8+dfsg-3) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libapt-pkg5.0_1.8.0_s390x.deb ... Unpacking libapt-pkg5.0:s390x (1.8.0) over (1.8.0~alpha2ubuntu1) ... Setting up libapt-pkg5.0:s390x (1.8.0) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libpam0g_1.3.1-5ubuntu1_s390x.deb ... Unpacking libpam0g:s390x (1.3.1-5ubuntu1) over (1.1.8-3.6ubuntu2) ... Setting up libpam0g:s390x (1.3.1-5ubuntu1) ... Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libsemanage-common_2.8-2_all.deb ... Unpacking libsemanage-common (2.8-2) over (2.8-1build2) ... Setting up libsemanage-common (2.8-2) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libsemanage1_2.8-2_s390x.deb ... Unpacking libsemanage1:s390x (2.8-2) over (2.8-1build2) ... Setting up libsemanage1:s390x (2.8-2) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.3.1-5ubuntu1_s390x.deb ... Unpacking libpam-modules-bin (1.3.1-5ubuntu1) over (1.1.8-3.6ubuntu2) ... Setting up libpam-modules-bin (1.3.1-5ubuntu1) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.3.1-5ubuntu1_s390x.deb ... Unpacking libpam-modules:s390x (1.3.1-5ubuntu1) over (1.1.8-3.6ubuntu2) ... Setting up libpam-modules:s390x (1.3.1-5ubuntu1) ... Installing new version of config file /etc/security/access.conf ... Installing new version of config file /etc/security/limits.conf ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.5-1.1ubuntu2_s390x.deb ... Unpacking passwd (1:4.5-1.1ubuntu2) over (1:4.5-1ubuntu1) ... Setting up passwd (1:4.5-1.1ubuntu2) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../adduser_3.118ubuntu1_all.deb ... Unpacking adduser (3.118ubuntu1) over (3.117ubuntu1) ... Setting up adduser (3.118ubuntu1) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.35-1_s390x.deb ... Unpacking libgpg-error0:s390x (1.35-1) over (1.32-3) ... Setting up libgpg-error0:s390x (1.35-1) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.12-1ubuntu3_s390x.deb ... Unpacking gpgv (2.2.12-1ubuntu3) over (2.2.8-3ubuntu1) ... Setting up gpgv (2.2.12-1ubuntu3) ... (Reading database ... 12486 files and directories currently installed.) Preparing to unpack .../archives/apt_1.8.0_s390x.deb ... Unpacking apt (1.8.0) over (1.8.0~alpha2ubuntu1) ... Setting up apt (1.8.0) ... (Reading database ... 12498 files and directories currently installed.) Preparing to unpack .../systemd-sysv_240-6ubuntu3_s390x.deb ... Unpacking systemd-sysv (240-6ubuntu3) over (239-7ubuntu15) ... Preparing to unpack .../libacl1_2.2.53-4_s390x.deb ... Unpacking libacl1:s390x (2.2.53-4) over (2.2.52-3build1) ... Setting up libacl1:s390x (2.2.53-4) ... (Reading database ... 12498 files and directories currently installed.) Preparing to unpack .../00-libapparmor1_2.13.2-9ubuntu5_s390x.deb ... Unpacking libapparmor1:s390x (2.13.2-9ubuntu5) over (2.12-4ubuntu10) ... Preparing to unpack .../01-libcap2_1%3a2.25-2_s390x.deb ... Unpacking libcap2:s390x (1:2.25-2) over (1:2.25-1.2) ... Preparing to unpack .../02-libargon2-1_0~20171227-0.2_s390x.deb ... Unpacking libargon2-1:s390x (0~20171227-0.2) over (0~20171227-0.1) ... Preparing to unpack .../03-libjson-c3_0.12.1+ds-2_s390x.deb ... Unpacking libjson-c3:s390x (0.12.1+ds-2) over (0.12.1-1.3) ... Preparing to unpack .../04-libssl1.1_1.1.1b-1ubuntu2_s390x.deb ... Unpacking libssl1.1:s390x (1.1.1b-1ubuntu2) over (1.1.1a-1ubuntu2) ... Preparing to unpack .../05-libcryptsetup12_2%3a2.1.0-1ubuntu1_s390x.deb ... Unpacking libcryptsetup12:s390x (2:2.1.0-1ubuntu1) over (2:2.0.4-2ubuntu2) ... Preparing to unpack .../06-libidn11_1.33-2.2ubuntu2_s390x.deb ... Unpacking libidn11:s390x (1.33-2.2ubuntu2) over (1.33-2.2ubuntu1) ... Preparing to unpack .../07-libkmod2_25-1ubuntu3_s390x.deb ... Unpacking libkmod2:s390x (25-1ubuntu3) over (25-1ubuntu2) ... Preparing to unpack .../08-mount_2.33.1-0.1ubuntu2_s390x.deb ... Unpacking mount (2.33.1-0.1ubuntu2) over (2.32-0.1ubuntu2) ... Preparing to unpack .../09-systemd_240-6ubuntu3_s390x.deb ... Unpacking systemd (240-6ubuntu3) over (239-7ubuntu15) ... Preparing to unpack .../10-libsystemd0_240-6ubuntu3_s390x.deb ... Unpacking libsystemd0:s390x (240-6ubuntu3) over (239-7ubuntu15) ... Setting up libsystemd0:s390x (240-6ubuntu3) ... (Reading database ... 12514 files and directories currently installed.) Preparing to unpack .../libext2fs2_1.44.6-1_s390x.deb ... Unpacking libext2fs2:s390x (1.44.6-1) over (1.44.4-2ubuntu1) ... Setting up libext2fs2:s390x (1.44.6-1) ... (Reading database ... 12513 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.44.6-1_s390x.deb ... Unpacking e2fsprogs (1.44.6-1) over (1.44.4-2ubuntu1) ... Setting up libapparmor1:s390x (2.13.2-9ubuntu5) ... Setting up libcap2:s390x (1:2.25-2) ... Setting up libargon2-1:s390x (0~20171227-0.2) ... Setting up libjson-c3:s390x (0.12.1+ds-2) ... Setting up libssl1.1:s390x (1.1.1b-1ubuntu2) ... Setting up libcryptsetup12:s390x (2:2.1.0-1ubuntu1) ... Setting up libidn11:s390x (1.33-2.2ubuntu2) ... Setting up libkmod2:s390x (25-1ubuntu3) ... Setting up util-linux (2.33.1-0.1ubuntu2) ... Setting up mount (2.33.1-0.1ubuntu2) ... Setting up systemd (240-6ubuntu3) ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/resolved.conf ... Installing new version of config file /etc/systemd/system.conf ... Setting up systemd-sysv (240-6ubuntu3) ... (Reading database ... 12513 files and directories currently installed.) Preparing to unpack .../init_1.56+nmu1_s390x.deb ... Unpacking init (1.56+nmu1) over (1.56) ... Preparing to unpack .../libattr1_1%3a2.4.48-4_s390x.deb ... Unpacking libattr1:s390x (1:2.4.48-4) over (1:2.4.47-2build1) ... Setting up libattr1:s390x (1:2.4.48-4) ... (Reading database ... 12514 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.7.9-2_s390x.deb ... Unpacking libcap-ng0:s390x (0.7.9-2) over (0.7.9-1build1) ... Setting up libcap-ng0:s390x (0.7.9-2) ... (Reading database ... 12514 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.3.1-5ubuntu1_all.deb ... Unpacking libpam-runtime (1.3.1-5ubuntu1) over (1.1.8-3.6ubuntu2) ... Setting up libpam-runtime (1.3.1-5ubuntu1) ... (Reading database ... 12514 files and directories currently installed.) Preparing to unpack .../libpcre3_2%3a8.39-12_s390x.deb ... Unpacking libpcre3:s390x (2:8.39-12) over (2:8.39-11) ... Setting up libpcre3:s390x (2:8.39-12) ... (Reading database ... 12514 files and directories currently installed.) Preparing to unpack .../00-libcom-err2_1.44.6-1_s390x.deb ... Unpacking libcom-err2:s390x (1.44.6-1) over (1.44.4-2ubuntu1) ... Preparing to unpack .../01-libprocps7_2%3a3.3.15-2ubuntu2_s390x.deb ... Unpacking libprocps7:s390x (2:3.3.15-2ubuntu2) over (2:3.3.15-2ubuntu1) ... Preparing to unpack .../02-libss2_1.44.6-1_s390x.deb ... Unpacking libss2:s390x (1.44.6-1) over (1.44.4-2ubuntu1) ... Preparing to unpack .../03-procps_2%3a3.3.15-2ubuntu2_s390x.deb ... Unpacking procps (2:3.3.15-2ubuntu2) over (2:3.3.15-2ubuntu1) ... Preparing to unpack .../04-openssl_1.1.1b-1ubuntu2_s390x.deb ... Unpacking openssl (1.1.1b-1ubuntu2) over (1.1.1a-1ubuntu2) ... Preparing to unpack .../05-ca-certificates_20190110_all.deb ... Unpacking ca-certificates (20190110) over (20180409) ... Preparing to unpack .../06-readline-common_8.0-1_all.deb ... Unpacking readline-common (8.0-1) over (7.0-5) ... Selecting previously unselected package libreadline8:s390x. Preparing to unpack .../07-libreadline8_8.0-1_s390x.deb ... Unpacking libreadline8:s390x (8.0-1) ... Preparing to unpack .../08-libsqlite3-0_3.27.2-2_s390x.deb ... Unpacking libsqlite3-0:s390x (3.27.2-2) over (3.26.0-2) ... Preparing to unpack .../09-tzdata_2019a-1_all.deb ... Unpacking tzdata (2019a-1) over (2018g-1) ... Preparing to unpack .../10-xz-utils_5.2.4-1_s390x.deb ... Unpacking xz-utils (5.2.4-1) over (5.2.2-1.3) ... Preparing to unpack .../11-libpng16-16_1.6.36-5_s390x.deb ... Unpacking libpng16-16:s390x (1.6.36-5) over (1.6.34-2) ... Preparing to unpack .../12-multiarch-support_2.29-0ubuntu2_s390x.deb ... Unpacking multiarch-support (2.29-0ubuntu2) over (2.28-0ubuntu1) ... Preparing to unpack .../13-binutils-s390x-linux-gnu_2.32-7ubuntu4_s390x.deb ... Unpacking binutils-s390x-linux-gnu (2.32-7ubuntu4) over (2.31.1-10ubuntu1) ... Preparing to unpack .../14-libbinutils_2.32-7ubuntu4_s390x.deb ... Unpacking libbinutils:s390x (2.32-7ubuntu4) over (2.31.1-10ubuntu1) ... Preparing to unpack .../15-binutils_2.32-7ubuntu4_s390x.deb ... Unpacking binutils (2.32-7ubuntu4) over (2.31.1-10ubuntu1) ... Preparing to unpack .../16-binutils-common_2.32-7ubuntu4_s390x.deb ... Unpacking binutils-common:s390x (2.32-7ubuntu4) over (2.31.1-10ubuntu1) ... Preparing to unpack .../17-libubsan1_9-20190402-1ubuntu1_s390x.deb ... Unpacking libubsan1:s390x (9-20190402-1ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../18-libgomp1_9-20190402-1ubuntu1_s390x.deb ... Unpacking libgomp1:s390x (9-20190402-1ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../19-libitm1_9-20190402-1ubuntu1_s390x.deb ... Unpacking libitm1:s390x (9-20190402-1ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../20-libatomic1_9-20190402-1ubuntu1_s390x.deb ... Unpacking libatomic1:s390x (9-20190402-1ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../21-libasan5_9-20190402-1ubuntu1_s390x.deb ... Unpacking libasan5:s390x (9-20190402-1ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../22-g++-8_8.3.0-6ubuntu1_s390x.deb ... Unpacking g++-8 (8.3.0-6ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../23-gcc-8_8.3.0-6ubuntu1_s390x.deb ... Unpacking gcc-8 (8.3.0-6ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../24-libstdc++-8-dev_8.3.0-6ubuntu1_s390x.deb ... Unpacking libstdc++-8-dev:s390x (8.3.0-6ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../25-libgcc-8-dev_8.3.0-6ubuntu1_s390x.deb ... Unpacking libgcc-8-dev:s390x (8.3.0-6ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../26-libcc1-0_9-20190402-1ubuntu1_s390x.deb ... Unpacking libcc1-0:s390x (9-20190402-1ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../27-cpp-8_8.3.0-6ubuntu1_s390x.deb ... Unpacking cpp-8 (8.3.0-6ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../28-gcc-8-base_8.3.0-6ubuntu1_s390x.deb ... Unpacking gcc-8-base:s390x (8.3.0-6ubuntu1) over (8.2.0-12ubuntu1) ... Preparing to unpack .../29-libmpfr6_4.0.2-1_s390x.deb ... Unpacking libmpfr6:s390x (4.0.2-1) over (4.0.1-2) ... Preparing to unpack .../30-g++_4%3a8.3.0-1ubuntu3_s390x.deb ... Unpacking g++ (4:8.3.0-1ubuntu3) over (4:8.2.0-2ubuntu2) ... Preparing to unpack .../31-gcc_4%3a8.3.0-1ubuntu3_s390x.deb ... Unpacking gcc (4:8.3.0-1ubuntu3) over (4:8.2.0-2ubuntu2) ... Preparing to unpack .../32-cpp_4%3a8.3.0-1ubuntu3_s390x.deb ... Unpacking cpp (4:8.3.0-1ubuntu3) over (4:8.2.0-2ubuntu2) ... Preparing to unpack .../33-dpkg-dev_1.19.6ubuntu1_all.deb ... Unpacking dpkg-dev (1.19.6ubuntu1) over (1.19.2ubuntu1) ... Preparing to unpack .../34-libdpkg-perl_1.19.6ubuntu1_all.deb ... Unpacking libdpkg-perl (1.19.6ubuntu1) over (1.19.2ubuntu1) ... Preparing to unpack .../35-build-essential_12.6ubuntu1_s390x.deb ... Unpacking build-essential (12.6ubuntu1) over (12.5ubuntu2) ... Preparing to unpack .../36-e2fslibs_1.44.6-1_s390x.deb ... Unpacking e2fslibs:s390x (1.44.6-1) over (1.44.4-2ubuntu1) ... Preparing to unpack .../37-libassuan0_2.5.2-1_s390x.deb ... Unpacking libassuan0:s390x (2.5.2-1) over (2.5.1-2) ... Preparing to unpack .../38-gpg_2.2.12-1ubuntu3_s390x.deb ... Unpacking gpg (2.2.12-1ubuntu3) over (2.2.8-3ubuntu1) ... Preparing to unpack .../39-gpgconf_2.2.12-1ubuntu3_s390x.deb ... Unpacking gpgconf (2.2.12-1ubuntu3) over (2.2.8-3ubuntu1) ... Preparing to unpack .../40-gpg-agent_2.2.12-1ubuntu3_s390x.deb ... Unpacking gpg-agent (2.2.12-1ubuntu3) over (2.2.8-3ubuntu1) ... Preparing to unpack .../41-libcomerr2_1.44.6-1_s390x.deb ... Unpacking libcomerr2:s390x (1.44.6-1) over (1.44.4-2ubuntu1) ... Preparing to unpack .../42-optipng_0.7.7-1_s390x.deb ... Unpacking optipng (0.7.7-1) over (0.7.6-1.1) ... Preparing to unpack .../43-pkgbinarymangler_144_all.deb ... Unpacking pkgbinarymangler (144) over (143) ... Setting up perl-modules-5.28 (5.28.1-6) ... Setting up lsb-base (10.2019031300ubuntu1) ... Setting up e2fslibs:s390x (1.44.6-1) ... Setting up init (1.56+nmu1) ... Setting up libprocps7:s390x (2:3.3.15-2ubuntu2) ... Setting up libsqlite3-0:s390x (3.27.2-2) ... Setting up binutils-common:s390x (2.32-7ubuntu4) ... Setting up linux-libc-dev:s390x (5.0.0-8.9) ... Setting up libcom-err2:s390x (1.44.6-1) ... Setting up libassuan0:s390x (2.5.2-1) ... Setting up libgomp1:s390x (9-20190402-1ubuntu1) ... Setting up tzdata (2019a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Apr 9 05:31:22 UTC 2019. Universal Time is now: Tue Apr 9 05:31:22 UTC 2019. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasan5:s390x (9-20190402-1ubuntu1) ... Setting up multiarch-support (2.29-0ubuntu2) ... Setting up libmpfr6:s390x (4.0.2-1) ... Setting up libncurses6:s390x (6.1+20181013-2ubuntu2) ... Setting up xz-utils (5.2.4-1) ... Setting up libpng16-16:s390x (1.6.36-5) ... Setting up libatomic1:s390x (9-20190402-1ubuntu1) ... Setting up libss2:s390x (1.44.6-1) ... Setting up gcc-8-base:s390x (8.3.0-6ubuntu1) ... Setting up libubsan1:s390x (9-20190402-1ubuntu1) ... Setting up libcomerr2:s390x (1.44.6-1) ... Setting up procps (2:3.3.15-2ubuntu2) ... Installing new version of config file /etc/sysctl.d/10-network-security.conf ... Setting up libbinutils:s390x (2.32-7ubuntu4) ... Setting up cpp-8 (8.3.0-6ubuntu1) ... Setting up libc-dev-bin (2.29-0ubuntu2) ... Setting up openssl (1.1.1b-1ubuntu2) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.0-1) ... Setting up libcc1-0:s390x (9-20190402-1ubuntu1) ... Setting up libitm1:s390x (9-20190402-1ubuntu1) ... Setting up libgdbm6:s390x (1.18.1-4) ... Setting up binutils-s390x-linux-gnu (2.32-7ubuntu4) ... Setting up libreadline8:s390x (8.0-1) ... Setting up e2fsprogs (1.44.6-1) ... Setting up binutils (2.32-7ubuntu4) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 2 added, 7 removed; done. Setting up optipng (0.7.7-1) ... Setting up libgdbm-compat4:s390x (1.18.1-4) ... Setting up libgcc-8-dev:s390x (8.3.0-6ubuntu1) ... Setting up libperl5.28:s390x (5.28.1-6) ... Setting up cpp (4:8.3.0-1ubuntu3) ... Setting up gpgconf (2.2.12-1ubuntu3) ... Setting up libc6-dev:s390x (2.29-0ubuntu2) ... Setting up gpg (2.2.12-1ubuntu3) ... Setting up libstdc++-8-dev:s390x (8.3.0-6ubuntu1) ... Setting up gcc-8 (8.3.0-6ubuntu1) ... Setting up gpg-agent (2.2.12-1ubuntu3) ... Setting up pkgbinarymangler (144) ... Setting up gcc (4:8.3.0-1ubuntu3) ... Setting up perl (5.28.1-6) ... Setting up libdpkg-perl (1.19.6ubuntu1) ... Setting up g++-8 (8.3.0-6ubuntu1) ... Setting up dpkg-dev (1.19.6ubuntu1) ... Setting up g++ (4:8.3.0-1ubuntu3) ... Setting up build-essential (12.6ubuntu1) ... Processing triggers for systemd (240-6ubuntu3) ... Processing triggers for libc-bin (2.29-0ubuntu2) ... Processing triggers for ca-certificates (20190110) ... 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/bin/sbuild-package PACKAGEBUILD-15625499 s390x disco-proposed -c chroot:build-PACKAGEBUILD-15625499 --arch=s390x --dist=disco-proposed --nolog bcftools_1.9-1.dsc Initiating build PACKAGEBUILD-15625499 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-145-generic #171-Ubuntu SMP Tue Mar 26 12:43:03 UTC 2019 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-s390x-019.buildd +==============================================================================+ | bcftools 1.9-1 (s390x) 09 Apr 2019 05:31 | +==============================================================================+ Package: bcftools Version: 1.9-1 Source Version: 1.9-1 Distribution: disco-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/bcftools-IXu8b9/bcftools-1.9' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-IXu8b9' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15625499/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bcftools_1.9-1.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-f2R6my/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-f2R6my/apt_archive ./ InRelease Get:2 copy:/<>/resolver-f2R6my/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-f2R6my/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-f2R6my/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-f2R6my/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (0 B/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 package was automatically installed and is no longer required: libreadline7 Use 'apt autoremove' to remove it. 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 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-f2R6my/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12574 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl Filtered Build-Depends: debhelper (>= 11~), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<>/resolver-S_EaOH/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. Ign:1 copy:/<>/resolver-S_EaOH/apt_archive ./ InRelease Get:2 copy:/<>/resolver-S_EaOH/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-S_EaOH/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-S_EaOH/apt_archive ./ Sources [271 B] Get:5 copy:/<>/resolver-S_EaOH/apt_archive ./ Packages [577 B] Fetched 2967 B in 0s (0 B/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 package was automatically installed and is no longer required: libreadline7 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libtool libuchardet0 libwind0-heimdal 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 krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 25.4 MB of archives. After this operation, 91.2 MB of additional disk space will be used. Get:1 copy:/<>/resolver-S_EaOH/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [904 B] Get:2 http://ftpmaster.internal/ubuntu disco/main s390x libbsd0 s390x 0.9.1-2 [43.0 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main s390x bsdmainutils s390x 11.1.2ubuntu2 [181 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main s390x libuchardet0 s390x 0.0.6-3 [64.5 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main s390x groff-base s390x 1.22.4-3 [819 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main s390x libpipeline1 s390x 1.5.1-2 [24.5 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main s390x man-db s390x 2.8.5-2 [1087 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main s390x libmagic-mgc s390x 1:5.35-4 [200 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main s390x libmagic1 s390x 1:5.35-4 [70.6 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main s390x file s390x 1:5.35-4 [22.7 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main s390x libelf1 s390x 0.176-1 [41.4 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main s390x libglib2.0-0 s390x 2.60.0-1 [1143 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main s390x libicu63 s390x 63.1-6 [8034 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main s390x libxml2 s390x 2.9.4+dfsg1-7ubuntu3 [553 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main s390x gettext-base s390x 0.19.8.1-9 [48.1 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main s390x libkrb5support0 s390x 1.17-1 [32.4 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main s390x libk5crypto3 s390x 1.17-1 [83.7 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main s390x libkeyutils1 s390x 1.6-6 [9816 B] Get:19 http://ftpmaster.internal/ubuntu disco/main s390x libkrb5-3 s390x 1.17-1 [308 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main s390x libgssapi-krb5-2 s390x 1.17-1 [111 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main s390x libpsl5 s390x 0.20.2-2 [49.8 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main s390x libsigsegv2 s390x 2.12-2 [13.8 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main s390x m4 s390x 1.4.18-2 [194 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main s390x autoconf all 2.69-11 [322 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main s390x autotools-dev all 20180224.1 [39.6 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main s390x automake all 1:1.16.1-4ubuntu3 [522 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main s390x autopoint all 0.19.8.1-9 [412 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main s390x libtool all 2.4.6-10 [194 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main s390x dh-autoreconf all 19 [16.1 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main s390x libarchive-zip-perl all 1.64-1 [84.9 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main s390x libfile-stripnondeterminism-perl all 1.1.2-1 [13.7 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main s390x dh-strip-nondeterminism all 1.1.2-1 [5208 B] Get:33 http://ftpmaster.internal/ubuntu disco/main s390x dwz s390x 0.12-3 [73.6 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main s390x libcroco3 s390x 0.6.12-3 [74.0 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main s390x gettext s390x 0.19.8.1-9 [858 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main s390x intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main s390x po-debconf all 1.0.21 [233 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main s390x debhelper all 12ubuntu1 [887 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main s390x libroken18-heimdal s390x 7.5.0+dfsg-2.1 [39.0 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main s390x libasn1-8-heimdal s390x 7.5.0+dfsg-2.1 [149 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main s390x libbz2-dev s390x 1.0.6-9 [30.6 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main s390x libheimbase1-heimdal s390x 7.5.0+dfsg-2.1 [27.5 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main s390x libhcrypto4-heimdal s390x 7.5.0+dfsg-2.1 [82.1 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main s390x libwind0-heimdal s390x 7.5.0+dfsg-2.1 [47.6 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main s390x libhx509-5-heimdal s390x 7.5.0+dfsg-2.1 [97.9 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main s390x libkrb5-26-heimdal s390x 7.5.0+dfsg-2.1 [189 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main s390x libheimntlm0-heimdal s390x 7.5.0+dfsg-2.1 [14.1 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main s390x libgssapi3-heimdal s390x 7.5.0+dfsg-2.1 [86.8 kB] Get:49 http://ftpmaster.internal/ubuntu disco/main s390x libsasl2-modules-db s390x 2.1.27+dfsg-1 [14.0 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main s390x libsasl2-2 s390x 2.1.27+dfsg-1 [46.4 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main s390x libldap-common all 2.4.47+dfsg-3ubuntu1 [16.5 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main s390x libldap-2.4-2 s390x 2.4.47+dfsg-3ubuntu1 [143 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main s390x libnghttp2-14 s390x 1.36.0-2 [75.1 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2 [51.1 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main s390x libssh-4 s390x 0.8.6-3 [175 kB] Get:56 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libcurl3-gnutls s390x 7.64.0-2ubuntu1 [210 kB] Get:57 http://ftpmaster.internal/ubuntu disco/universe s390x libdeflate0 s390x 1.2-1 [52.4 kB] Get:58 http://ftpmaster.internal/ubuntu disco/universe s390x libgslcblas0 s390x 2.5+dfsg-6 [72.7 kB] Get:59 http://ftpmaster.internal/ubuntu disco/universe s390x libgsl23 s390x 2.5+dfsg-6 [747 kB] Get:60 http://ftpmaster.internal/ubuntu disco/universe s390x libgsl-dev s390x 2.5+dfsg-6 [934 kB] Get:61 http://ftpmaster.internal/ubuntu disco/universe s390x libhts2 s390x 1.9-10 [268 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main s390x liblzma-dev s390x 5.2.4-1 [145 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main s390x zlib1g-dev s390x 1:1.2.11.dfsg-1ubuntu2 [170 kB] Get:64 http://ftpmaster.internal/ubuntu disco/universe s390x libhts-dev s390x 1.9-10 [4334 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main s390x libio-pty-perl s390x 1:1.08-1.1build5 [29.4 kB] Get:66 http://ftpmaster.internal/ubuntu disco/universe s390x tabix s390x 1.9-10 [253 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.4 MB in 1s (29.7 MB/s) Selecting previously unselected package libbsd0:s390x. (Reading database ... 12574 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_s390x.deb ... Unpacking libbsd0:s390x (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu2_s390x.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package libuchardet0:s390x. Preparing to unpack .../02-libuchardet0_0.0.6-3_s390x.deb ... Unpacking libuchardet0:s390x (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_s390x.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../04-libpipeline1_1.5.1-2_s390x.deb ... Unpacking libpipeline1:s390x (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_s390x.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.35-4_s390x.deb ... Unpacking libmagic-mgc (1:5.35-4) ... Selecting previously unselected package libmagic1:s390x. Preparing to unpack .../07-libmagic1_1%3a5.35-4_s390x.deb ... Unpacking libmagic1:s390x (1:5.35-4) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.35-4_s390x.deb ... Unpacking file (1:5.35-4) ... Selecting previously unselected package libelf1:s390x. Preparing to unpack .../09-libelf1_0.176-1_s390x.deb ... Unpacking libelf1:s390x (0.176-1) ... Selecting previously unselected package libglib2.0-0:s390x. Preparing to unpack .../10-libglib2.0-0_2.60.0-1_s390x.deb ... Unpacking libglib2.0-0:s390x (2.60.0-1) ... Selecting previously unselected package libicu63:s390x. Preparing to unpack .../11-libicu63_63.1-6_s390x.deb ... Unpacking libicu63:s390x (63.1-6) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../12-libxml2_2.9.4+dfsg1-7ubuntu3_s390x.deb ... Unpacking libxml2:s390x (2.9.4+dfsg1-7ubuntu3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../13-gettext-base_0.19.8.1-9_s390x.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libkrb5support0:s390x. Preparing to unpack .../14-libkrb5support0_1.17-1_s390x.deb ... Unpacking libkrb5support0:s390x (1.17-1) ... Selecting previously unselected package libk5crypto3:s390x. Preparing to unpack .../15-libk5crypto3_1.17-1_s390x.deb ... Unpacking libk5crypto3:s390x (1.17-1) ... Selecting previously unselected package libkeyutils1:s390x. Preparing to unpack .../16-libkeyutils1_1.6-6_s390x.deb ... Unpacking libkeyutils1:s390x (1.6-6) ... Selecting previously unselected package libkrb5-3:s390x. Preparing to unpack .../17-libkrb5-3_1.17-1_s390x.deb ... Unpacking libkrb5-3:s390x (1.17-1) ... Selecting previously unselected package libgssapi-krb5-2:s390x. Preparing to unpack .../18-libgssapi-krb5-2_1.17-1_s390x.deb ... Unpacking libgssapi-krb5-2:s390x (1.17-1) ... Selecting previously unselected package libpsl5:s390x. Preparing to unpack .../19-libpsl5_0.20.2-2_s390x.deb ... Unpacking libpsl5:s390x (0.20.2-2) ... Selecting previously unselected package libsigsegv2:s390x. Preparing to unpack .../20-libsigsegv2_2.12-2_s390x.deb ... Unpacking libsigsegv2:s390x (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../21-m4_1.4.18-2_s390x.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../22-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../23-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../24-automake_1%3a1.16.1-4ubuntu3_all.deb ... Unpacking automake (1:1.16.1-4ubuntu3) ... Selecting previously unselected package autopoint. Preparing to unpack .../25-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../26-libtool_2.4.6-10_all.deb ... Unpacking libtool (2.4.6-10) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../27-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../28-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../29-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../30-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package dwz. Preparing to unpack .../31-dwz_0.12-3_s390x.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libcroco3:s390x. Preparing to unpack .../32-libcroco3_0.6.12-3_s390x.deb ... Unpacking libcroco3:s390x (0.6.12-3) ... Selecting previously unselected package gettext. Preparing to unpack .../33-gettext_0.19.8.1-9_s390x.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../34-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../35-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../36-debhelper_12ubuntu1_all.deb ... Unpacking debhelper (12ubuntu1) ... Selecting previously unselected package libroken18-heimdal:s390x. Preparing to unpack .../37-libroken18-heimdal_7.5.0+dfsg-2.1_s390x.deb ... Unpacking libroken18-heimdal:s390x (7.5.0+dfsg-2.1) ... Selecting previously unselected package libasn1-8-heimdal:s390x. Preparing to unpack .../38-libasn1-8-heimdal_7.5.0+dfsg-2.1_s390x.deb ... Unpacking libasn1-8-heimdal:s390x (7.5.0+dfsg-2.1) ... Selecting previously unselected package libbz2-dev:s390x. Preparing to unpack .../39-libbz2-dev_1.0.6-9_s390x.deb ... Unpacking libbz2-dev:s390x (1.0.6-9) ... Selecting previously unselected package libheimbase1-heimdal:s390x. Preparing to unpack .../40-libheimbase1-heimdal_7.5.0+dfsg-2.1_s390x.deb ... Unpacking libheimbase1-heimdal:s390x (7.5.0+dfsg-2.1) ... Selecting previously unselected package libhcrypto4-heimdal:s390x. Preparing to unpack .../41-libhcrypto4-heimdal_7.5.0+dfsg-2.1_s390x.deb ... Unpacking libhcrypto4-heimdal:s390x (7.5.0+dfsg-2.1) ... Selecting previously unselected package libwind0-heimdal:s390x. Preparing to unpack .../42-libwind0-heimdal_7.5.0+dfsg-2.1_s390x.deb ... Unpacking libwind0-heimdal:s390x (7.5.0+dfsg-2.1) ... Selecting previously unselected package libhx509-5-heimdal:s390x. Preparing to unpack .../43-libhx509-5-heimdal_7.5.0+dfsg-2.1_s390x.deb ... Unpacking libhx509-5-heimdal:s390x (7.5.0+dfsg-2.1) ... Selecting previously unselected package libkrb5-26-heimdal:s390x. Preparing to unpack .../44-libkrb5-26-heimdal_7.5.0+dfsg-2.1_s390x.deb ... Unpacking libkrb5-26-heimdal:s390x (7.5.0+dfsg-2.1) ... Selecting previously unselected package libheimntlm0-heimdal:s390x. Preparing to unpack .../45-libheimntlm0-heimdal_7.5.0+dfsg-2.1_s390x.deb ... Unpacking libheimntlm0-heimdal:s390x (7.5.0+dfsg-2.1) ... Selecting previously unselected package libgssapi3-heimdal:s390x. Preparing to unpack .../46-libgssapi3-heimdal_7.5.0+dfsg-2.1_s390x.deb ... Unpacking libgssapi3-heimdal:s390x (7.5.0+dfsg-2.1) ... Selecting previously unselected package libsasl2-modules-db:s390x. Preparing to unpack .../47-libsasl2-modules-db_2.1.27+dfsg-1_s390x.deb ... Unpacking libsasl2-modules-db:s390x (2.1.27+dfsg-1) ... Selecting previously unselected package libsasl2-2:s390x. Preparing to unpack .../48-libsasl2-2_2.1.27+dfsg-1_s390x.deb ... Unpacking libsasl2-2:s390x (2.1.27+dfsg-1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../49-libldap-common_2.4.47+dfsg-3ubuntu1_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3ubuntu1) ... Selecting previously unselected package libldap-2.4-2:s390x. Preparing to unpack .../50-libldap-2.4-2_2.4.47+dfsg-3ubuntu1_s390x.deb ... Unpacking libldap-2.4-2:s390x (2.4.47+dfsg-3ubuntu1) ... Selecting previously unselected package libnghttp2-14:s390x. Preparing to unpack .../51-libnghttp2-14_1.36.0-2_s390x.deb ... Unpacking libnghttp2-14:s390x (1.36.0-2) ... Selecting previously unselected package librtmp1:s390x. Preparing to unpack .../52-librtmp1_2.4+20151223.gitfa8646d.1-2_s390x.deb ... Unpacking librtmp1:s390x (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh-4:s390x. Preparing to unpack .../53-libssh-4_0.8.6-3_s390x.deb ... Unpacking libssh-4:s390x (0.8.6-3) ... Selecting previously unselected package libcurl3-gnutls:s390x. Preparing to unpack .../54-libcurl3-gnutls_7.64.0-2ubuntu1_s390x.deb ... Unpacking libcurl3-gnutls:s390x (7.64.0-2ubuntu1) ... Selecting previously unselected package libdeflate0:s390x. Preparing to unpack .../55-libdeflate0_1.2-1_s390x.deb ... Unpacking libdeflate0:s390x (1.2-1) ... Selecting previously unselected package libgslcblas0:s390x. Preparing to unpack .../56-libgslcblas0_2.5+dfsg-6_s390x.deb ... Unpacking libgslcblas0:s390x (2.5+dfsg-6) ... Selecting previously unselected package libgsl23:s390x. Preparing to unpack .../57-libgsl23_2.5+dfsg-6_s390x.deb ... Unpacking libgsl23:s390x (2.5+dfsg-6) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../58-libgsl-dev_2.5+dfsg-6_s390x.deb ... Unpacking libgsl-dev (2.5+dfsg-6) ... Selecting previously unselected package libhts2:s390x. Preparing to unpack .../59-libhts2_1.9-10_s390x.deb ... Unpacking libhts2:s390x (1.9-10) ... Selecting previously unselected package liblzma-dev:s390x. Preparing to unpack .../60-liblzma-dev_5.2.4-1_s390x.deb ... Unpacking liblzma-dev:s390x (5.2.4-1) ... Selecting previously unselected package zlib1g-dev:s390x. Preparing to unpack .../61-zlib1g-dev_1%3a1.2.11.dfsg-1ubuntu2_s390x.deb ... Unpacking zlib1g-dev:s390x (1:1.2.11.dfsg-1ubuntu2) ... Selecting previously unselected package libhts-dev:s390x. Preparing to unpack .../62-libhts-dev_1.9-10_s390x.deb ... Unpacking libhts-dev:s390x (1.9-10) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../63-libio-pty-perl_1%3a1.08-1.1build5_s390x.deb ... Unpacking libio-pty-perl (1:1.08-1.1build5) ... Selecting previously unselected package tabix. Preparing to unpack .../64-tabix_1.9-10_s390x.deb ... Unpacking tabix (1.9-10) ... Selecting previously unselected package sbuild-build-depends-bcftools-dummy. Preparing to unpack .../65-sbuild-build-depends-bcftools-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Setting up libpipeline1:s390x (1.5.1-2) ... Setting up libkeyutils1:s390x (1.6-6) ... Setting up libpsl5:s390x (0.20.2-2) ... Setting up libgslcblas0:s390x (2.5+dfsg-6) ... Setting up libio-pty-perl (1:1.08-1.1build5) ... Setting up libmagic-mgc (1:5.35-4) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:s390x (2.60.0-1) ... No schema files found: doing nothing. Setting up libnghttp2-14:s390x (1.36.0-2) ... Setting up libmagic1:s390x (1:5.35-4) ... Setting up libdeflate0:s390x (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4) ... Setting up libldap-common (2.4.47+dfsg-3ubuntu1) ... Setting up libicu63:s390x (63.1-6) ... Setting up libkrb5support0:s390x (1.17-1) ... Setting up libsasl2-modules-db:s390x (2.1.27+dfsg-1) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2) ... Setting up libgsl23:s390x (2.5+dfsg-6) ... Setting up libsigsegv2:s390x (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:s390x (1.17-1) ... Setting up libsasl2-2:s390x (2.1.27+dfsg-1) ... Setting up libroken18-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up liblzma-dev:s390x (5.2.4-1) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-1ubuntu2) ... Setting up libuchardet0:s390x (0.0.6-3) ... Setting up libkrb5-3:s390x (1.17-1) ... Setting up libbsd0:s390x (0.9.1-2) ... Setting up libelf1:s390x (0.176-1) ... Setting up libxml2:s390x (2.9.4+dfsg1-7ubuntu3) ... Setting up libheimbase1-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up libbz2-dev:s390x (1.0.6-9) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libgsl-dev (2.5+dfsg-6) ... Setting up libtool (2.4.6-10) ... Setting up libasn1-8-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up m4 (1.4.18-2) ... Setting up libhcrypto4-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up libwind0-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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 libgssapi-krb5-2:s390x (1.17-1) ... Setting up libcroco3:s390x (0.6.12-3) ... Setting up libssh-4:s390x (0.8.6-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libhx509-5-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libkrb5-26-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up po-debconf (1.0.21) ... Setting up libheimntlm0-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up libgssapi3-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up libldap-2.4-2:s390x (2.4.47+dfsg-3ubuntu1) ... Setting up libcurl3-gnutls:s390x (7.64.0-2ubuntu1) ... Setting up tabix (1.9-10) ... Setting up libhts2:s390x (1.9-10) ... Setting up libhts-dev:s390x (1.9-10) ... Setting up debhelper (12ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.29-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-145-generic s390x (s390x) Toolchain package versions: binutils_2.32-7ubuntu4 dpkg-dev_1.19.6ubuntu1 g++-8_8.3.0-6ubuntu1 gcc-8_8.3.0-6ubuntu1 libc6-dev_2.29-0ubuntu2 libstdc++-8-dev_8.3.0-6ubuntu1 libstdc++6_9-20190402-1ubuntu1 linux-libc-dev_5.0.0-8.9 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-1 apt_1.8.0 autoconf_2.69-11 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.46 bash_5.0-3ubuntu1 binutils_2.32-7ubuntu4 binutils-common_2.32-7ubuntu4 binutils-s390x-linux-gnu_2.32-7ubuntu4 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.33.1-0.1ubuntu2 build-essential_12.6ubuntu1 bzip2_1.0.6-9 ca-certificates_20190110 coreutils_8.30-1ubuntu1 cpp_4:8.3.0-1ubuntu3 cpp-8_8.3.0-6ubuntu1 dash_0.5.10.2-4ubuntu1 debconf_1.5.71 debhelper_12ubuntu1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-2 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.6ubuntu1 dpkg-dev_1.19.6ubuntu1 dwz_0.12-3 e2fslibs_1.44.6-1 e2fsprogs_1.44.6-1 fakeroot_1.23-1 fdisk_2.33.1-0.1ubuntu2 file_1:5.35-4 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1ubuntu3 g++-8_8.3.0-6ubuntu1 gcc_4:8.3.0-1ubuntu3 gcc-8_8.3.0-6ubuntu1 gcc-8-base_8.3.0-6ubuntu1 gcc-9-base_9-20190402-1ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpg_2.2.12-1ubuntu3 gpg-agent_2.2.12-1ubuntu3 gpgconf_2.2.12-1ubuntu3 gpgv_2.2.12-1ubuntu3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 init_1.56+nmu1 init-system-helpers_1.56+nmu1 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapparmor1_2.13.2-9ubuntu5 libapt-pkg5.0_1.8.0 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.2 libasan5_9-20190402-1ubuntu1 libasn1-8-heimdal_7.5.0+dfsg-2.1 libassuan0_2.5.2-1 libatomic1_9-20190402-1ubuntu1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbinutils_2.32-7ubuntu4 libblkid1_2.33.1-0.1ubuntu2 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9 libbz2-dev_1.0.6-9 libc-bin_2.29-0ubuntu2 libc-dev-bin_2.29-0ubuntu2 libc6_2.29-0ubuntu2 libc6-dev_2.29-0ubuntu2 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_9-20190402-1ubuntu1 libcom-err2_1.44.6-1 libcomerr2_1.44.6-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.1.0-1ubuntu1 libcurl3-gnutls_7.64.0-2ubuntu1 libdb5.3_5.3.28+dfsg1-0.5 libdebconfclient0_0.247ubuntu1 libdeflate0_1.2-1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.6ubuntu1 libelf1_0.176-1 libext2fs2_1.44.6-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1ubuntu2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.2-1 libgcc-8-dev_8.3.0-6ubuntu1 libgcc1_1:9-20190402-1ubuntu1 libgcrypt20_1.8.4-3ubuntu1 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libglib2.0-0_2.60.0-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2ubuntu1 libgomp1_9-20190402-1ubuntu1 libgpg-error0_1.35-1 libgsl-dev_2.5+dfsg-6 libgsl23_2.5+dfsg-6 libgslcblas0_2.5+dfsg-6 libgssapi-krb5-2_1.17-1 libgssapi3-heimdal_7.5.0+dfsg-2.1 libhcrypto4-heimdal_7.5.0+dfsg-2.1 libheimbase1-heimdal_7.5.0+dfsg-2.1 libheimntlm0-heimdal_7.5.0+dfsg-2.1 libhogweed4_3.4.1-1 libhts-dev_1.9-10 libhts2_1.9-10 libhx509-5-heimdal_7.5.0+dfsg-2.1 libicu63_63.1-6 libidn11_1.33-2.2ubuntu2 libidn2-0_2.0.5-1 libio-pty-perl_1:1.08-1.1build5 libip4tc0_1.6.1-2ubuntu3 libisl19_0.20-2 libitm1_9-20190402-1ubuntu1 libjson-c3_0.12.1+ds-2 libk5crypto3_1.17-1 libkeyutils1_1.6-6 libkmod2_25-1ubuntu3 libkrb5-26-heimdal_7.5.0+dfsg-2.1 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libldap-2.4-2_2.4.47+dfsg-3ubuntu1 libldap-common_2.4.47+dfsg-3ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblz4-1_1.8.3-1ubuntu1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmount1_2.33.1-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.1+20181013-2ubuntu2 libncursesw6_6.1+20181013-2ubuntu2 libnettle6_3.4.1-1 libnghttp2-14_1.36.0-2 libnpth0_1.6-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5ubuntu1 libpam-modules-bin_1.3.1-5ubuntu1 libpam-runtime_1.3.1-5ubuntu1 libpam0g_1.3.1-5ubuntu1 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpng16-16_1.6.36-5 libprocps7_2:3.3.15-2ubuntu2 libpsl5_0.20.2-2 libreadline7_7.0-5 libreadline8_8.0-1 libroken18-heimdal_7.5.0+dfsg-2.1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.33.1-0.1ubuntu2 libsqlite3-0_3.27.2-2 libss2_1.44.6-1 libssh-4_0.8.6-3 libssl1.1_1.1.1b-1ubuntu2 libstdc++-8-dev_8.3.0-6ubuntu1 libstdc++6_9-20190402-1ubuntu1 libsystemd0_240-6ubuntu3 libtasn1-6_4.13-3 libtinfo6_6.1+20181013-2ubuntu2 libtool_2.4.6-10 libubsan1_9-20190402-1ubuntu1 libuchardet0_0.0.6-3 libudev1_240-6ubuntu3 libunistring2_0.9.10-1ubuntu2 libusb-0.1-4_2:0.1.12-32 libustr-1.0-1_1.0.4-6 libuuid1_2.33.1-0.1ubuntu2 libwind0-heimdal_7.5.0+dfsg-2.1 libxml2_2.9.4+dfsg1-7ubuntu3 libzstd1_1.3.8+dfsg-3 linux-libc-dev_5.0.0-8.9 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu2 lsb-base_10.2019031300ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17ubuntu3 mount_2.33.1-0.1ubuntu2 multiarch-support_2.29-0ubuntu2 ncurses-base_6.1+20181013-2ubuntu2 ncurses-bin_6.1+20181013-2ubuntu2 openssl_1.1.1b-1ubuntu2 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu2 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-1build2 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu2 readline-common_8.0-1 sbuild-build-depends-bcftools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-6ubuntu3 systemd-sysv_240-6ubuntu3 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tabix_1.9-10 tar_1.30+dfsg-5 tzdata_2019a-1 ubuntu-keyring_2018.09.18.1 util-linux_2.33.1-0.1ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu2 zlib1g-dev_1:1.2.11.dfsg-1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Sep 4 14:47:28 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.9-1.dsc dpkg-source: info: extracting bcftools in bcftools-1.9 dpkg-source: info: unpacking bcftools_1.9.orig.tar.gz dpkg-source: info: unpacking bcftools_1.9-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.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-15625499 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15625499 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15625499 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 1.9-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean rm -f config.mk && touch config.mk dh clean 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 config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/<>' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/<>' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/s390x-linux-gnu/bcftools ./configure --build=s390x-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/s390x-linux-gnu --libexecdir=\${prefix}/lib/s390x-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/s390x-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/<>' dh_auto_build -a make -j4 make[1]: Entering directory '/<>' echo '#define BCFTOOLS_VERSION "1.9"' > version.h gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c vcfmerge.c: In function ‘merge_vcf’: vcfmerge.c:2334:46: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] char buf[10]; snprintf(buf,10,"%d",i+1); ^ In file included from /usr/include/stdio.h:867, from vcfmerge.c:25: /usr/include/s390x-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 10 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/s390x-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/split.so version.c plugins/split.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl gcc -rdynamic -pthread -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 vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o ccall.o em.o prob1.o kmin.o -lhts -lm -lz -ldl -ldl make[1]: Leaving directory '/<>' dh_auto_test -a make -j4 test VERBOSE=1 make[1]: Entering directory '/<>' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec 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 sort .. 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 roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/r6aZ6kfDIt/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/r6aZ6kfDIt/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/r6aZ6kfDIt/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/r6aZ6kfDIt/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/r6aZ6kfDIt/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/r6aZ6kfDIt/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/r6aZ6kfDIt/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/r6aZ6kfDIt/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/r6aZ6kfDIt/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/r6aZ6kfDIt/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/r6aZ6kfDIt/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/r6aZ6kfDIt/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/r6aZ6kfDIt/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/r6aZ6kfDIt/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/r6aZ6kfDIt/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/r6aZ6kfDIt/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/r6aZ6kfDIt/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/r6aZ6kfDIt/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/r6aZ6kfDIt/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/r6aZ6kfDIt/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/r6aZ6kfDIt/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/r6aZ6kfDIt/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/r6aZ6kfDIt/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/r6aZ6kfDIt/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/r6aZ6kfDIt/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/r6aZ6kfDIt/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/r6aZ6kfDIt/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/check.1.chk /tmp/r6aZ6kfDIt/check.2.chk /tmp/r6aZ6kfDIt/check.3.chk /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/stats.a.vcf.gz /tmp/r6aZ6kfDIt/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/r6aZ6kfDIt/stats.a.vcf.gz /tmp/r6aZ6kfDIt/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/r6aZ6kfDIt/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/r6aZ6kfDIt/isec.a.vcf.gz /tmp/r6aZ6kfDIt/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/r6aZ6kfDIt/isec.a.vcf.gz /tmp/r6aZ6kfDIt/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/r6aZ6kfDIt/isec.a.vcf.gz /tmp/r6aZ6kfDIt/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/r6aZ6kfDIt/isec.a.vcf.gz /tmp/r6aZ6kfDIt/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/r6aZ6kfDIt/isec.a.vcf.gz /tmp/r6aZ6kfDIt/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/r6aZ6kfDIt/isec.a.vcf.gz /tmp/r6aZ6kfDIt/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/r6aZ6kfDIt/isec.a.vcf.gz /tmp/r6aZ6kfDIt/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/r6aZ6kfDIt/isec.a.vcf.gz /tmp/r6aZ6kfDIt/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/r6aZ6kfDIt/isec.a.vcf.gz /tmp/r6aZ6kfDIt/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/r6aZ6kfDIt/isec.a.vcf.gz /tmp/r6aZ6kfDIt/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/r6aZ6kfDIt/isec.tab.gz /tmp/r6aZ6kfDIt/isec.a.vcf.gz 2>/dev/null The outputs differ: /<>/test/isec.tab.out /<>/test/isec.tab.out.new .. failed ... test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/r6aZ6kfDIt/isec.tab.gz /tmp/r6aZ6kfDIt/isec.a.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/isec.tab.out /<>/test/isec.tab.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/r6aZ6kfDIt/merge.a.vcf.gz /tmp/r6aZ6kfDIt/merge.b.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.a.vcf.gz /tmp/r6aZ6kfDIt/merge.b.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.a.vcf.gz /tmp/r6aZ6kfDIt/merge.b.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.a.vcf.gz /tmp/r6aZ6kfDIt/merge.b.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.a.vcf.gz /tmp/r6aZ6kfDIt/merge.b.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.a.vcf.gz /tmp/r6aZ6kfDIt/merge.b.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.2.a.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.2.a.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.2.a.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.2.a.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.2.a.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.2.a.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.3.a.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.3.a.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.4.a.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.4.a.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/gvcf.merge.1.vcf.gz /tmp/r6aZ6kfDIt/gvcf.merge.2.vcf.gz /tmp/r6aZ6kfDIt/gvcf.merge.3.vcf.gz The outputs differ: /<>/test/gvcf.merge.1.out /<>/test/gvcf.merge.1.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/r6aZ6kfDIt/gvcf.merge.1.vcf.gz /tmp/r6aZ6kfDIt/gvcf.merge.2.vcf.gz /tmp/r6aZ6kfDIt/gvcf.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/gvcf.merge.1.out /<>/test/gvcf.merge.1.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/r6aZ6kfDIt/merge.gvcf.2.a.vcf.gz /tmp/r6aZ6kfDIt/merge.gvcf.2.b.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/merge.gvcf.2.a.vcf.gz /tmp/r6aZ6kfDIt/merge.gvcf.2.b.vcf.gz /tmp/r6aZ6kfDIt/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 --gvcf - -i SRC:join /tmp/r6aZ6kfDIt/merge.gvcf.3.a.vcf.gz /tmp/r6aZ6kfDIt/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/r6aZ6kfDIt/merge.gvcf.3.a.vcf.gz /tmp/r6aZ6kfDIt/merge.gvcf.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/r6aZ6kfDIt/merge.5.a.vcf.gz /tmp/r6aZ6kfDIt/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/r6aZ6kfDIt/merge.5.a.vcf.gz /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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" && XGS!="."' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/r6aZ6kfDIt/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/view.vectors.vcf.gz The outputs differ: /<>/test/query.12.out /<>/test/query.12.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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' The outputs differ: /<>/test/query.12.out /<>/test/query.12.out.new .. failed ... test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/r6aZ6kfDIt/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/r6aZ6kfDIt/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/r6aZ6kfDIt/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/r6aZ6kfDIt/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/r6aZ6kfDIt/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/missing.vcf.gz | /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/r6aZ6kfDIt/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/r6aZ6kfDIt/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.filter.2.vcf.gz | /<>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/r6aZ6kfDIt/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/filter.5.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/r6aZ6kfDIt/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/filter.5.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/r6aZ6kfDIt/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.filter.3.vcf.gz | /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/r6aZ6kfDIt/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.filter.3.vcf.gz | /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/r6aZ6kfDIt/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.filter.3.vcf.gz | /<>/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/r6aZ6kfDIt/query.filter.4.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.filter.4.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /<>/bcftools query -f'%ID\n' -i 'ID=@/<>/test/query.56.out' /tmp/r6aZ6kfDIt/view.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.vcf.gz | /<>/bcftools query -f'%ID\n' -i 'ID=@/<>/test/query.56.out' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/r6aZ6kfDIt/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.filter.5.vcf.gz | /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/r6aZ6kfDIt/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.filter.5.vcf.gz | /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/r6aZ6kfDIt/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/query.filter.5.vcf.gz | /<>/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx -f /<>/test/norm.fa /tmp/r6aZ6kfDIt/norm.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.out /<>/test/norm.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -cx -f /<>/test/norm.fa /tmp/r6aZ6kfDIt/norm.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.out /<>/test/norm.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ [E::bcf_record_check] Bad BCF record - shared section malformed or too short The outputs differ: /<>/test/norm.split.out /<>/test/norm.split.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/r6aZ6kfDIt/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/norm.split.vcf.gz 2>/dev/null Non-zero status 255 .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m- -f /<>/test/norm.fa /tmp/r6aZ6kfDIt/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ Failed to open -: unknown file type Non-zero status 1 .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/r6aZ6kfDIt/norm.merge.vcf.gz 2>/dev/null Non-zero status 1 .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/r6aZ6kfDIt/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ [E::bcf_record_check] Bad BCF record - shared section malformed or too short The outputs differ: /<>/test/norm.merge.out /<>/test/norm.merge.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/r6aZ6kfDIt/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/r6aZ6kfDIt/norm.merge.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/r6aZ6kfDIt/norm.merge.3.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/r6aZ6kfDIt/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 '.' .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/r6aZ6kfDIt/norm.merge.vcf.gz 2>/dev/null /bin/bash: line 1: 12686 Segmentation fault (core dumped) /<>/bcftools norm --no-version -m+ -s /tmp/r6aZ6kfDIt/norm.merge.vcf.gz 2> /dev/null Non-zero status 139 .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ -s /tmp/r6aZ6kfDIt/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ [E::bcf_record_check] Bad BCF record - shared section malformed or too short 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/r6aZ6kfDIt/norm.setref.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/norm.telomere.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/r6aZ6kfDIt/norm.telomere.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/r6aZ6kfDIt/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d snps /tmp/r6aZ6kfDIt/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/r6aZ6kfDIt/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d indels /tmp/r6aZ6kfDIt/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/r6aZ6kfDIt/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d both /tmp/r6aZ6kfDIt/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/r6aZ6kfDIt/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d all /tmp/r6aZ6kfDIt/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/r6aZ6kfDIt/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d none /tmp/r6aZ6kfDIt/norm.rmdup.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/r6aZ6kfDIt/view.vcf.gz The outputs differ: /<>/test/view.1.out /<>/test/view.1.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/r6aZ6kfDIt/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.1.out /<>/test/view.1.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/r6aZ6kfDIt/view.vcf.gz -r20,Y The outputs differ: /<>/test/view.2.out /<>/test/view.2.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/r6aZ6kfDIt/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.2.out /<>/test/view.2.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/r6aZ6kfDIt/view.vcf.gz The outputs differ: /<>/test/view.3.out /<>/test/view.3.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/r6aZ6kfDIt/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.3.out /<>/test/view.3.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/r6aZ6kfDIt/view.vcf.gz The outputs differ: /<>/test/view.4.out /<>/test/view.4.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/r6aZ6kfDIt/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.4.out /<>/test/view.4.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -p /tmp/r6aZ6kfDIt/view.vcf.gz The outputs differ: /<>/test/view.5.out /<>/test/view.5.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -p /tmp/r6aZ6kfDIt/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.5.out /<>/test/view.5.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -P /tmp/r6aZ6kfDIt/view.vcf.gz The outputs differ: /<>/test/view.6.out /<>/test/view.6.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -P /tmp/r6aZ6kfDIt/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.6.out /<>/test/view.6.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/r6aZ6kfDIt/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/r6aZ6kfDIt/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/r6aZ6kfDIt/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/r6aZ6kfDIt/view.vcf.gz The outputs differ: /<>/test/view.9.out /<>/test/view.9.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/r6aZ6kfDIt/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.9.out /<>/test/view.9.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/r6aZ6kfDIt/view.vcf.gz The outputs differ: /<>/test/view.10.out /<>/test/view.10.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/r6aZ6kfDIt/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.10.out /<>/test/view.10.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/r6aZ6kfDIt/view.vcf.gz The outputs differ: /<>/test/view.exclude.out /<>/test/view.exclude.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/r6aZ6kfDIt/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.exclude.out /<>/test/view.exclude.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version /tmp/r6aZ6kfDIt/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/r6aZ6kfDIt/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/r6aZ6kfDIt/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/r6aZ6kfDIt/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/r6aZ6kfDIt/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/r6aZ6kfDIt/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/r6aZ6kfDIt/view.vectors.vcf.gz The outputs differ: /<>/test/view.vectors.A.out /<>/test/view.vectors.A.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -asA /tmp/r6aZ6kfDIt/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.vectors.A.out /<>/test/view.vectors.A.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -asB /tmp/r6aZ6kfDIt/view.vectors.vcf.gz The outputs differ: /<>/test/view.vectors.B.out /<>/test/view.vectors.B.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -asB /tmp/r6aZ6kfDIt/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/view.vectors.B.out /<>/test/view.vectors.B.out.new .. failed ... test_vcf_view: /<>/bcftools view --no-version -asA /tmp/r6aZ6kfDIt/view.vectors.2.vcf.gz [E::bcf_remove_allele_set] Unexpected number of values in INFO/IAF at 1:10; expected Number=A=2, but found 1 Error: Could not trim alleles at 1:10 Non-zero status 255 .. failed ... test_vcf_view: /<>/bcftools view -Ob -asA /tmp/r6aZ6kfDIt/view.vectors.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ [E::bcf_remove_allele_set] Unexpected number of values in INFO/IAF at 1:10; expected Number=A=2, but found 1 Error: Could not trim alleles at 1:10 Failed to open -: unknown file type Non-zero status 1 .. failed ... test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/r6aZ6kfDIt/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/r6aZ6kfDIt/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/r6aZ6kfDIt/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/r6aZ6kfDIt/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/r6aZ6kfDIt/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/r6aZ6kfDIt/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/r6aZ6kfDIt/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/r6aZ6kfDIt/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/r6aZ6kfDIt/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 The outputs differ: /<>/test/mpileup.2.out /<>/test/mpileup.2.out.new .. failed ... test_vcf_call: /<>/bcftools call -Ob -mg0 /<>/test/mpileup.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/mpileup.2.out /<>/test/mpileup.2.out.new .. failed ... 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/r6aZ6kfDIt/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/r6aZ6kfDIt/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_ The outputs differ: /<>/test/filter.1.out /<>/test/filter.1.out.new .. failed ... test_vcf_filter: /<>/bcftools filter -Ob -mx -g2 -G2 /<>/test/filter.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/filter.1.out /<>/test/filter.1.out.new .. failed ... 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'INFO/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'INFO/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'INFO/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'INFO/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'INFO/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'INFO/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'INFO/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'INFO/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'INFO/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'INFO/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_filter: /<>/bcftools filter -i'GT="A"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="A"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="RR"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="RR"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="RA"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="RA"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="AR"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="AR"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="AA"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="AA"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="aA"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="aA"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="Aa"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="Aa"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="HOM"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="HOM"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="HET"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="HET"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="HAP"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="HAP"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[:1]=11' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[:1]=11' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[1:]=11' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[1:]=11' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'FR[0:1]=11' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'FR[0:1]=11' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[*]="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[*]="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[0:0]=="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[0:0]=="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[0:0]!="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[0:0]!="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'QUAL=="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'QUAL=="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /<>/bcftools filter -i'N_PASS(DP>32)=1' /<>/test/filter.2.vcf | /<>/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'N_PASS(DP>32)=1' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /<>/bcftools filter -i'F_PASS(DP>32)=0.5' /<>/test/filter.2.vcf | /<>/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_sort: /<>/bcftools sort -m 0 /<>/test/sort.vcf | /<>/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.HRBpYT Merging 17 temporary files Cleaning Done .. ok test_vcf_sort: /<>/bcftools sort -Ob -m 0 /<>/test/sort.vcf | /<>/bcftools view | /<>/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.ukFIPS Merging 17 temporary files Cleaning Done .. ok test_vcf_sort: /<>/bcftools sort -m 1000 /<>/test/sort.vcf | /<>/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.OAH1kW Merging 5 temporary files Cleaning Done .. ok test_vcf_sort: /<>/bcftools sort -Ob -m 1000 /<>/test/sort.vcf | /<>/bcftools view | /<>/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.DmEdxV Merging 5 temporary files Cleaning Done .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab /tmp/r6aZ6kfDIt/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/r6aZ6kfDIt/regions.tab.gz /tmp/r6aZ6kfDIt/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/r6aZ6kfDIt/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/r6aZ6kfDIt/regions.tab.gz /tmp/r6aZ6kfDIt/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/r6aZ6kfDIt/regions.bed /tmp/r6aZ6kfDIt/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/r6aZ6kfDIt/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/r6aZ6kfDIt/regions.bed /tmp/r6aZ6kfDIt/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/r6aZ6kfDIt/regions.bed.gz /tmp/r6aZ6kfDIt/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/r6aZ6kfDIt/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/r6aZ6kfDIt/regions.bed.gz /tmp/r6aZ6kfDIt/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/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/r6aZ6kfDIt/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/r6aZ6kfDIt/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/r6aZ6kfDIt/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/r6aZ6kfDIt/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/r6aZ6kfDIt/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/r6aZ6kfDIt/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/r6aZ6kfDIt/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/r6aZ6kfDIt/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/r6aZ6kfDIt/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/r6aZ6kfDIt/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/r6aZ6kfDIt/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/r6aZ6kfDIt/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/r6aZ6kfDIt/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/annots4.vcf.gz -c +INFO /tmp/r6aZ6kfDIt/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/r6aZ6kfDIt/annots4.vcf.gz -c +INFO /tmp/r6aZ6kfDIt/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/r6aZ6kfDIt/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_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/r6aZ6kfDIt/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_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/r6aZ6kfDIt/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_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/r6aZ6kfDIt/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_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/r6aZ6kfDIt/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/r6aZ6kfDIt/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/r6aZ6kfDIt/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/r6aZ6kfDIt/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/r6aZ6kfDIt/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_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/r6aZ6kfDIt/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_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/r6aZ6kfDIt/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/r6aZ6kfDIt/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/r6aZ6kfDIt/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/r6aZ6kfDIt/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/r6aZ6kfDIt/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/r6aZ6kfDIt/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/r6aZ6kfDIt/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/r6aZ6kfDIt/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/r6aZ6kfDIt/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/r6aZ6kfDIt/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/r6aZ6kfDIt/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/r6aZ6kfDIt/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/r6aZ6kfDIt/annots11.vcf.gz -c FMT /tmp/r6aZ6kfDIt/annotate11.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/r6aZ6kfDIt/annots11.vcf.gz -c FMT /tmp/r6aZ6kfDIt/annotate11.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +missing2ref --no-version /tmp/r6aZ6kfDIt/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +missing2ref --no-version /tmp/r6aZ6kfDIt/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/r6aZ6kfDIt/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/r6aZ6kfDIt/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/r6aZ6kfDIt/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/r6aZ6kfDIt/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/r6aZ6kfDIt/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/<>/test/setGT.samples.txt]="het"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/r6aZ6kfDIt/setGT.2.bcf -- -t q -n . -i 'GT[@/<>/test/setGT.samples.txt]="het"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/r6aZ6kfDIt/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/<>/test/setGT.samples.txt]="het" & binom(AD[@/<>/test/setGT.samples.txt])<0.1' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/r6aZ6kfDIt/setGT.2.bcf -- -t q -n . -i 'GT[@/<>/test/setGT.samples.txt]="het" & binom(AD[@/<>/test/setGT.samples.txt])<0.1' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-AN-AC --no-version /tmp/r6aZ6kfDIt/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-AN-AC --no-version /tmp/r6aZ6kfDIt/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +dosage /tmp/r6aZ6kfDIt/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +dosage /tmp/r6aZ6kfDIt/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixploidy --no-version /tmp/r6aZ6kfDIt/fixploidy.vcf.gz -- -s /<>/test/fixploidy.samples -p /<>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixploidy --no-version /tmp/r6aZ6kfDIt/fixploidy.bcf -- -s /<>/test/fixploidy.samples -p /<>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/r6aZ6kfDIt/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/r6aZ6kfDIt/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/r6aZ6kfDIt/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ Warning: PL tag not found in header, switching to GL .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/r6aZ6kfDIt/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ Warning: PL tag not found in header, switching to GL .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/r6aZ6kfDIt/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/r6aZ6kfDIt/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/r6aZ6kfDIt/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/r6aZ6kfDIt/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/r6aZ6kfDIt/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/r6aZ6kfDIt/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/r6aZ6kfDIt/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/fill-tags.2.out /<>/test/fill-tags.2.out.new .. failed ... test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/r6aZ6kfDIt/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/fill-tags.2.out /<>/test/fill-tags.2.out.new .. failed ... test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/r6aZ6kfDIt/view.vcf.gz -- -t AC -S /<>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/fill-tags.3.out /<>/test/fill-tags.3.out.new .. failed ... test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/r6aZ6kfDIt/view.bcf -- -t AC -S /<>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/fill-tags.3.out /<>/test/fill-tags.3.out.new .. failed ... test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/r6aZ6kfDIt/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/r6aZ6kfDIt/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/r6aZ6kfDIt/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/r6aZ6kfDIt/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/r6aZ6kfDIt/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +trio-switch-rate /tmp/r6aZ6kfDIt/trio.vcf.gz -- -p /<>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +trio-switch-rate /tmp/r6aZ6kfDIt/trio.bcf -- -p /<>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +trio-stats /tmp/r6aZ6kfDIt/trio-stats.vcf.gz -p /<>/test/trio-stats.ped | grep -v ^CMD 2>/dev/null | grep -v ^##bcftools_ Identified 2 complete trios in the VCF file .. ok test_vcf_plugin: /<>/bcftools +trio-stats /tmp/r6aZ6kfDIt/trio-stats.bcf -p /<>/test/trio-stats.ped | grep -v ^CMD 2>/dev/null | grep -v ^##bcftools_ Identified 2 complete trios in the VCF file .. ok test_vcf_plugin: /<>/bcftools +ad-bias /tmp/r6aZ6kfDIt/ad-bias.vcf.gz -- -s /<>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +ad-bias /tmp/r6aZ6kfDIt/ad-bias.bcf -- -s /<>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +af-dist /tmp/r6aZ6kfDIt/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +af-dist /tmp/r6aZ6kfDIt/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixref /tmp/r6aZ6kfDIt/fixref.2a.vcf.gz -- -f /<>/test/norm.fa -i /tmp/r6aZ6kfDIt/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixref /tmp/r6aZ6kfDIt/fixref.2a.bcf -- -f /<>/test/norm.fa -i /tmp/r6aZ6kfDIt/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixref /tmp/r6aZ6kfDIt/fixref.3.vcf.gz -- -f /<>/test/fixref.3.fa -m top 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixref /tmp/r6aZ6kfDIt/fixref.3.bcf -- -f /<>/test/fixref.3.fa -m top 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/r6aZ6kfDIt/aa.vcf.gz -- -f /<>/test/aa.fa -c AA -h /<>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_ Non-zero status 1 .. failed ... [E::bcf_record_check] Bad BCF record - shared section malformed or too short test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/r6aZ6kfDIt/aa.bcf -- -f /<>/test/aa.fa -c AA -h /<>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/aa.out /<>/test/aa.out.new .. failed ... test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/r6aZ6kfDIt/ref.vcf.gz -- -f /<>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ Non-zero status 1 .. failed ... [E::bcf_record_check] Bad BCF record - shared section malformed or too short test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/r6aZ6kfDIt/ref.bcf -- -f /<>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/ref.out /<>/test/ref.out.new .. failed ... test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/r6aZ6kfDIt/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/view.GTsubset.NA1.out /<>/test/view.GTsubset.NA1.out.new .. failed ... test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/r6aZ6kfDIt/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/view.GTsubset.NA1.out /<>/test/view.GTsubset.NA1.out.new .. failed ... test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/r6aZ6kfDIt/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/view.GTsubset.NA1NA2.out /<>/test/view.GTsubset.NA1NA2.out.new .. failed ... test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/r6aZ6kfDIt/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/view.GTsubset.NA1NA2.out /<>/test/view.GTsubset.NA1NA2.out.new .. failed ... test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/r6aZ6kfDIt/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/view.GTsubset.NA1NA2NA3.out /<>/test/view.GTsubset.NA1NA2NA3.out.new .. failed ... test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/r6aZ6kfDIt/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ The outputs differ: /<>/test/view.GTsubset.NA1NA2NA3.out /<>/test/view.GTsubset.NA1NA2NA3.out.new .. failed ... test_vcf_plugin: /<>/bcftools +mendelian /tmp/r6aZ6kfDIt/mendelian.vcf.gz -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/r6aZ6kfDIt/mendelian.bcf -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/r6aZ6kfDIt/mendelian.vcf.gz -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/r6aZ6kfDIt/mendelian.bcf -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/r6aZ6kfDIt/mendelian.vcf.gz -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/r6aZ6kfDIt/mendelian.bcf -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +contrast /tmp/r6aZ6kfDIt/contrast.vcf.gz -0 a,b -1 c 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +contrast /tmp/r6aZ6kfDIt/contrast.bcf -0 a,b -1 c 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/r6aZ6kfDIt/concat.1.a.vcf.gz /tmp/r6aZ6kfDIt/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/r6aZ6kfDIt/concat.1.a.vcf.gz /tmp/r6aZ6kfDIt/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/concat.1.vcf.out /<>/test/concat.1.vcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat --no-version /tmp/r6aZ6kfDIt/concat.1.a.bcf /tmp/r6aZ6kfDIt/concat.1.b.bcf The outputs differ: /<>/test/concat.1.bcf.out /<>/test/concat.1.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob /tmp/r6aZ6kfDIt/concat.1.a.bcf /tmp/r6aZ6kfDIt/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/concat.1.bcf.out /<>/test/concat.1.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/r6aZ6kfDIt/concat.2.a.vcf.gz /tmp/r6aZ6kfDIt/concat.2.b.vcf.gz The outputs differ: /<>/test/concat.2.vcf.out /<>/test/concat.2.vcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/r6aZ6kfDIt/concat.2.a.vcf.gz /tmp/r6aZ6kfDIt/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/concat.2.vcf.out /<>/test/concat.2.vcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/r6aZ6kfDIt/concat.2.a.bcf /tmp/r6aZ6kfDIt/concat.2.b.bcf The outputs differ: /<>/test/concat.2.bcf.out /<>/test/concat.2.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/r6aZ6kfDIt/concat.2.a.bcf /tmp/r6aZ6kfDIt/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/concat.2.bcf.out /<>/test/concat.2.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/r6aZ6kfDIt/concat.2.a.vcf.gz /tmp/r6aZ6kfDIt/concat.2.b.vcf.gz The outputs differ: /<>/test/concat.4.vcf.out /<>/test/concat.4.vcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/r6aZ6kfDIt/concat.2.a.vcf.gz /tmp/r6aZ6kfDIt/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/concat.4.vcf.out /<>/test/concat.4.vcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/r6aZ6kfDIt/concat.2.a.bcf /tmp/r6aZ6kfDIt/concat.2.b.bcf The outputs differ: /<>/test/concat.4.bcf.out /<>/test/concat.4.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/r6aZ6kfDIt/concat.2.a.bcf /tmp/r6aZ6kfDIt/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/concat.4.bcf.out /<>/test/concat.4.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/r6aZ6kfDIt/concat.3.a.vcf.gz /tmp/r6aZ6kfDIt/concat.3.b.vcf.gz /tmp/r6aZ6kfDIt/concat.3.0.vcf.gz /tmp/r6aZ6kfDIt/concat.3.c.vcf.gz /tmp/r6aZ6kfDIt/concat.3.d.vcf.gz /tmp/r6aZ6kfDIt/concat.3.e.vcf.gz /tmp/r6aZ6kfDIt/concat.3.f.vcf.gz [E::vcf_format] Invalid BCF, the FORMAT tag id=-13056 not present in the header The outputs differ: /<>/test/concat.3.vcf.out /<>/test/concat.3.vcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/r6aZ6kfDIt/concat.3.a.vcf.gz /tmp/r6aZ6kfDIt/concat.3.b.vcf.gz /tmp/r6aZ6kfDIt/concat.3.0.vcf.gz /tmp/r6aZ6kfDIt/concat.3.c.vcf.gz /tmp/r6aZ6kfDIt/concat.3.d.vcf.gz /tmp/r6aZ6kfDIt/concat.3.e.vcf.gz /tmp/r6aZ6kfDIt/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ GT is not present at 2:280. (This warning is printed only once.) [W::bcf_record_check] Bad BCF record: Invalid FORMAT id -13056 The outputs differ: /<>/test/concat.3.vcf.out /<>/test/concat.3.vcf.out.new .. failed ... [W::bcf_record_check] Bad BCF record: Invalid INFO id -14336 [W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080 test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/r6aZ6kfDIt/concat.3.a.bcf /tmp/r6aZ6kfDIt/concat.3.b.bcf /tmp/r6aZ6kfDIt/concat.3.0.bcf /tmp/r6aZ6kfDIt/concat.3.c.bcf /tmp/r6aZ6kfDIt/concat.3.d.bcf /tmp/r6aZ6kfDIt/concat.3.e.bcf /tmp/r6aZ6kfDIt/concat.3.f.bcf [W::bcf_record_check] Bad BCF record: Invalid INFO id -14336 [W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080 [E::vcf_format] Invalid BCF, the FORMAT tag id=-13056 not present in the header The outputs differ: /<>/test/concat.3.bcf.out /<>/test/concat.3.bcf.out.new .. failed ... test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/r6aZ6kfDIt/concat.3.a.bcf /tmp/r6aZ6kfDIt/concat.3.b.bcf /tmp/r6aZ6kfDIt/concat.3.0.bcf /tmp/r6aZ6kfDIt/concat.3.c.bcf /tmp/r6aZ6kfDIt/concat.3.d.bcf /tmp/r6aZ6kfDIt/concat.3.e.bcf /tmp/r6aZ6kfDIt/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ [W::bcf_record_check] Bad BCF record: Invalid INFO id -14336 [W::bcf_record_check] Bad BCF record: Invalid FORMAT id -14080 [W::bcf_record_check] Bad BCF record: Invalid FORMAT id -13056 Random seed for test_naive_concat: 435121828 The outputs differ: /<>/test/concat.3.bcf.out /<>/test/concat.3.bcf.out.new .. failed ... test_naive_concat: /<>/bcftools concat --naive /tmp/r6aZ6kfDIt/naive_concat.0.bcf /tmp/r6aZ6kfDIt/naive_concat.1.bcf /tmp/r6aZ6kfDIt/naive_concat.2.bcf /tmp/r6aZ6kfDIt/naive_concat.3.bcf /tmp/r6aZ6kfDIt/naive_concat.4.bcf /tmp/r6aZ6kfDIt/naive_concat.5.bcf /tmp/r6aZ6kfDIt/naive_concat.6.bcf /tmp/r6aZ6kfDIt/naive_concat.7.bcf /tmp/r6aZ6kfDIt/naive_concat.8.bcf /tmp/r6aZ6kfDIt/naive_concat.9.bcf | /<>/bcftools view -H Failed to open -: unknown file type Non-zero status 255 .. failed ... test_naive_concat: /<>/bcftools concat --naive /tmp/r6aZ6kfDIt/naive_concat.0.vcf.gz /tmp/r6aZ6kfDIt/naive_concat.1.vcf.gz /tmp/r6aZ6kfDIt/naive_concat.2.vcf.gz /tmp/r6aZ6kfDIt/naive_concat.3.vcf.gz /tmp/r6aZ6kfDIt/naive_concat.4.vcf.gz /tmp/r6aZ6kfDIt/naive_concat.5.vcf.gz /tmp/r6aZ6kfDIt/naive_concat.6.vcf.gz /tmp/r6aZ6kfDIt/naive_concat.7.vcf.gz /tmp/r6aZ6kfDIt/naive_concat.8.vcf.gz /tmp/r6aZ6kfDIt/naive_concat.9.vcf.gz | /<>/bcftools view -H The outputs differ: /<>/test/concat.naive.vcf.out /<>/test/concat.naive.vcf.out.new .. failed ... 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/r6aZ6kfDIt/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/r6aZ6kfDIt/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/r6aZ6kfDIt/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/r6aZ6kfDIt/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/r6aZ6kfDIt/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/r6aZ6kfDIt/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/r6aZ6kfDIt/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/r6aZ6kfDIt/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/r6aZ6kfDIt/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/r6aZ6kfDIt/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/r6aZ6kfDIt/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/r6aZ6kfDIt/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/r6aZ6kfDIt/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/r6aZ6kfDIt/empty.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/r6aZ6kfDIt/rename.map -Ov /tmp/r6aZ6kfDIt/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/r6aZ6kfDIt/rename.map -Ob /tmp/r6aZ6kfDIt/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/r6aZ6kfDIt/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/r6aZ6kfDIt/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/r6aZ6kfDIt/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/convert.vcf.gz | /<>/bcftools convert -g -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/r6aZ6kfDIt/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/convert.vcf.gz | /<>/bcftools convert -g .,- 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/r6aZ6kfDIt/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/r6aZ6kfDIt/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/r6aZ6kfDIt/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/r6aZ6kfDIt/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/r6aZ6kfDIt/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/check.vcf.gz | /<>/bcftools convert -g -,. --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/r6aZ6kfDIt/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/check.vcf.gz | /<>/bcftools convert -g .,- --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/r6aZ6kfDIt/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/r6aZ6kfDIt/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/r6aZ6kfDIt/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/convert.vcf.gz | /<>/bcftools convert -h -,.,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/r6aZ6kfDIt/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/convert.vcf.gz | /<>/bcftools convert -h .,-,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/r6aZ6kfDIt/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/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 ^## The outputs differ: /<>/test/convert.gt.noHead.vcf /<>/test/convert.gt.noHead.vcf.new .. failed ... 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 ^## The outputs differ: /<>/test/convert.gt.noHead.vcf /<>/test/convert.gt.noHead.vcf.new .. failed ... test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples 2>/dev/null | grep -v ^## The outputs differ: /<>/test/convert.gt.noHead.vcf /<>/test/convert.gt.noHead.vcf.new .. failed ... 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 ^## The outputs differ: /<>/test/convert.gt.noHead.vcf /<>/test/convert.gt.noHead.vcf.new .. failed ... test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/r6aZ6kfDIt/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/convert.vcf.gz | /<>/bcftools convert --hapsample -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/r6aZ6kfDIt/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/convert.vcf.gz | /<>/bcftools convert --hapsample .,- 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert --haplegendsample -,.,. /tmp/r6aZ6kfDIt/convert.hap-missing.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/convert.hap-missing.vcf.gz | /<>/bcftools convert --haplegendsample -,.,. 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /<>/test/gvcf.fa /tmp/r6aZ6kfDIt/convert.gvcf.vcf.gz 2>/dev/null The outputs differ: /<>/test/convert.gvcf.out /<>/test/convert.gvcf.out.new .. failed ... test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/r6aZ6kfDIt/convert.gvcf.vcf.gz | /<>/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /<>/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools The outputs differ: /<>/test/convert.gvcf.out /<>/test/convert.gvcf.out.new .. failed ... 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/r6aZ6kfDIt/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/r6aZ6kfDIt/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/r6aZ6kfDIt/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/r6aZ6kfDIt/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/r6aZ6kfDIt/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/r6aZ6kfDIt/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/r6aZ6kfDIt/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/r6aZ6kfDIt/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/r6aZ6kfDIt/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/r6aZ6kfDIt/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab -c /tmp/r6aZ6kfDIt/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/r6aZ6kfDIt/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/r6aZ6kfDIt/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/r6aZ6kfDIt/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/r6aZ6kfDIt/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/r6aZ6kfDIt/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/r6aZ6kfDIt/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/r6aZ6kfDIt/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/r6aZ6kfDIt/empty.vcf.gz -f /<>/test/consensus.fa 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/r6aZ6kfDIt/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" 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/r6aZ6kfDIt/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/r6aZ6kfDIt/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/r6aZ6kfDIt/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/r6aZ6kfDIt/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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... 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 The outputs differ: /<>/test/mpileup/mpileup.6.out /<>/test/mpileup/mpileup.6.out.new .. failed ... 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 .. ok 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 .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok 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 .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa /<>/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa -Ob /<>/test/mpileup/indel-AD.1.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa /<>/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa -Ob /<>/test/mpileup/indel-AD.1.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok 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... The outputs differ: /<>/test/csq.1.out /<>/test/csq.1.out.new .. failed ... 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/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/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/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... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String The outputs differ: /<>/test/csq/ENST00000301246/15bp-insert.txt /<>/test/csq/ENST00000301246/15bp-insert.txt.new .. failed ... 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/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/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... /bin/bash: line 1: 14815 Done /<>/bcftools csq -f /<>/test/csq/ENST00000624631/ENST00000624631.fa -g /<>/test/csq/ENST00000624631/ENST00000624631.gff /<>/test/csq/ENST00000624631/ambiguous.vcf 14816 | /<>/test/csq/sort-csq 14817 Segmentation fault (core dumped) | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Non-zero status 139 .. failed ... test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000303039/ENST00000303039.fa -g /<>/test/csq/ENST00000303039/ENST00000303039.gff /<>/test/csq/ENST00000303039/not-a-stop.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000303039/ENST00000303039.fa -g /<>/test/csq/ENST00000303039/ENST00000303039.gff /<>/test/csq/ENST00000303039/not-a-stop.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/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/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... [E::vcf_format] Invalid BCF, the INFO index is too large The outputs differ: /<>/test/csq/ENST00000410009/frameshift.txt /<>/test/csq/ENST00000410009/frameshift.txt.new .. failed ... 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/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/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 The outputs differ: /<>/test/csq/ENST00000381157/haploid-diploid.txt /<>/test/csq/ENST00000381157/haploid-diploid.txt.new .. failed ... 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/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-donor4.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/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... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String The outputs differ: /<>/test/csq/ENST00000341065/frame3.txt /<>/test/csq/ENST00000341065/frame3.txt.new .. failed ... 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... [E::vcf_format] Invalid BCF, the INFO index is too large The outputs differ: /<>/test/csq/ENST00000341065/frame3.txt-l /<>/test/csq/ENST00000341065/frame3.txt-l.new .. failed ... 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-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/splice-acceptor-donor8.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... The outputs differ: /<>/test/csq/ENST00000341065/frame1.txt /<>/test/csq/ENST00000341065/frame1.txt.new .. failed ... 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... The outputs differ: /<>/test/csq/ENST00000341065/frame1.txt-l /<>/test/csq/ENST00000341065/frame1.txt-l.new .. failed ... 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/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... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String The outputs differ: /<>/test/csq/ENST00000341065/frame2.txt /<>/test/csq/ENST00000341065/frame2.txt.new .. failed ... 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... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String The outputs differ: /<>/test/csq/ENST00000341065/frame2.txt-l /<>/test/csq/ENST00000341065/frame2.txt-l.new .. failed ... 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-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/ENST00000271583/ENST00000271583.fa -g /<>/test/csq/ENST00000271583/ENST00000271583.gff /<>/test/csq/ENST00000271583/splice-acceptor.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/ENST00000271583/ENST00000271583.gff ... Indexed 1 transcripts, 11 exons, 11 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/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... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String The outputs differ: /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt.new .. failed ... 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... [E::vcf_format] Invalid BCF, the INFO index is too large The outputs differ: /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l.new .. failed ... 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/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/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/ENST00000557788/ENST00000557788.fa -g /<>/test/csq/ENST00000557788/ENST00000557788.gff /<>/test/csq/ENST00000557788/long-overlap-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000557788/ENST00000557788.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000368801/ENST00000368801.fa -g /<>/test/csq/ENST00000368801/ENST00000368801.gff /<>/test/csq/ENST00000368801/compound-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000368801/ENST00000368801.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs Calling... [E::vcf_format] Invalid BCF, the INFO index is too large The outputs differ: /<>/test/csq/ENST00000368801/compound-lost.txt /<>/test/csq/ENST00000368801/compound-lost.txt.new .. failed ... 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/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/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/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/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/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/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/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/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/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/ENST00000218032/ENST00000218032.fa -g /<>/test/csq/ENST00000218032/ENST00000218032.gff /<>/test/csq/ENST00000218032/start-lost-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/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 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/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/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/ENST00000378322/ENST00000378322.fa -g /<>/test/csq/ENST00000378322/ENST00000378322.gff /<>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000378322/ENST00000378322.fa -g /<>/test/csq/ENST00000378322/ENST00000378322.gff /<>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/insert3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/insert3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/snps.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/snps.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/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 Number of tests: total .. 821 passed .. 700 failed .. 121 make[1]: *** [Makefile:253: test-plugins] Error 1 make[1]: Leaving directory '/<>' dh_auto_test: make -j4 test VERBOSE=1 returned exit code 2 make: *** [debian/rules:7: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20190409-0532 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 32944 Build-Time: 41 Distribution: disco-proposed Fail-Stage: build Host Architecture: s390x Install-Time: 8 Job: bcftools_1.9-1.dsc Machine Architecture: s390x Package: bcftools Package-Time: 50 Source-Version: 1.9-1 Space: 32944 Status: attempted Version: 1.9-1 -------------------------------------------------------------------------------- Finished at 20190409-0532 Build needed 00:00:50, 32944k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=disco --arch=s390x PACKAGEBUILD-15625499 Scanning for processes to kill in build PACKAGEBUILD-15625499