https://launchpad.net/ubuntu/+archive/test-rebuild-20190906/+build/17534378 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-008 4.4.0-161-generic #189-Ubuntu SMP Tue Aug 27 08:09:43 UTC 2019 s390x Buildd toolchain package versions: launchpad-buildd_177 python-lpbuildd_177 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_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 14 Sep 17:21:03 ntpdate[1850]: adjust time server 10.211.37.1 offset 0.000271 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=eoan --arch=s390x PACKAGEBUILD-17534378 --image-type chroot /home/buildd/filecache-default/9c1cd73f9613a153d05a179bf4eae2e7ab569110 Creating target for build PACKAGEBUILD-17534378 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=eoan --arch=s390x PACKAGEBUILD-17534378 Starting target for build PACKAGEBUILD-17534378 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=eoan --arch=s390x PACKAGEBUILD-17534378 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan main' 'deb http://ftpmaster.internal/ubuntu eoan main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-17534378 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=eoan --arch=s390x PACKAGEBUILD-17534378 Adding trusted keys to build-PACKAGEBUILD-17534378 Warning: apt-key output should not be parsed (stdout is not a terminal) OK Warning: apt-key output should not be parsed (stdout is not a terminal) /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-archive.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 790B C727 7767 219C 42C8 6F93 3B4F E6AC C0B2 1F32 uid [ unknown] Ubuntu Archive Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=eoan --arch=s390x PACKAGEBUILD-17534378 Updating target for build PACKAGEBUILD-17534378 Get:1 http://ftpmaster.internal/ubuntu eoan InRelease [255 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan InRelease [15.4 kB] Get:3 http://ftpmaster.internal/ubuntu eoan/main s390x Packages [921 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan/main s390x Packages [2804 B] Get:5 http://ftpmaster.internal/ubuntu eoan/main Translation-en [505 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan/main Translation-en [4848 B] Get:7 http://ftpmaster.internal/ubuntu eoan/restricted s390x Packages [1064 B] Get:8 http://ftpmaster.internal/ubuntu eoan/restricted Translation-en [4836 B] Get:9 http://ftpmaster.internal/ubuntu eoan/universe s390x Packages [8502 kB] Get:10 http://ftpmaster.internal/ubuntu eoan/universe Translation-en [5221 kB] Get:11 http://ftpmaster.internal/ubuntu eoan/multiverse s390x Packages [119 kB] Get:12 http://ftpmaster.internal/ubuntu eoan/multiverse Translation-en [111 kB] Fetched 15.7 MB in 3s (5253 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: logsave The following packages will be upgraded: binutils binutils-common binutils-s390x-linux-gnu build-essential coreutils cpp cpp-9 dpkg dpkg-dev e2fsprogs g++ g++-9 gcc gcc-9 gcc-9-base libapparmor1 libasan5 libatomic1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcom-err2 libdevmapper1.02.1 libdpkg-perl libext2fs2 libgcc-9-dev libgcc1 libgnutls30 libgomp1 libisl21 libitm1 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libubsan1 linux-libc-dev login passwd 42 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 41.7 MB of archives. After this operation, 896 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu eoan/main s390x coreutils s390x 8.30-3ubuntu2 [1230 kB] Get:2 http://ftpmaster.internal/ubuntu eoan/main s390x dpkg s390x 1.19.7ubuntu2 [1106 kB] Get:3 http://ftpmaster.internal/ubuntu eoan/main s390x login s390x 1:4.5-1.1ubuntu4 [260 kB] Get:4 http://ftpmaster.internal/ubuntu eoan/main s390x libc6-dev s390x 2.30-0ubuntu1 [2054 kB] Get:5 http://ftpmaster.internal/ubuntu eoan/main s390x libc-dev-bin s390x 2.30-0ubuntu1 [63.1 kB] Get:6 http://ftpmaster.internal/ubuntu eoan/main s390x linux-libc-dev s390x 5.3.0-10.11 [1059 kB] Get:7 http://ftpmaster.internal/ubuntu eoan/main s390x libcc1-0 s390x 9.2.1-8ubuntu1 [45.5 kB] Get:8 http://ftpmaster.internal/ubuntu eoan/main s390x binutils-s390x-linux-gnu s390x 2.32.51.20190905-0ubuntu1 [1460 kB] Get:9 http://ftpmaster.internal/ubuntu eoan/main s390x libbinutils s390x 2.32.51.20190905-0ubuntu1 [299 kB] Get:10 http://ftpmaster.internal/ubuntu eoan/main s390x binutils-common s390x 2.32.51.20190905-0ubuntu1 [203 kB] Get:11 http://ftpmaster.internal/ubuntu eoan/main s390x binutils s390x 2.32.51.20190905-0ubuntu1 [3336 B] Get:12 http://ftpmaster.internal/ubuntu eoan/main s390x gcc-9-base s390x 9.2.1-8ubuntu1 [19.2 kB] Get:13 http://ftpmaster.internal/ubuntu eoan/main s390x libgcc1 s390x 1:9.2.1-8ubuntu1 [24.4 kB] Get:14 http://ftpmaster.internal/ubuntu eoan/main s390x libgomp1 s390x 9.2.1-8ubuntu1 [82.0 kB] Get:15 http://ftpmaster.internal/ubuntu eoan/main s390x libitm1 s390x 9.2.1-8ubuntu1 [26.8 kB] Get:16 http://ftpmaster.internal/ubuntu eoan/main s390x libatomic1 s390x 9.2.1-8ubuntu1 [8412 B] Get:17 http://ftpmaster.internal/ubuntu eoan/main s390x libasan5 s390x 9.2.1-8ubuntu1 [349 kB] Get:18 http://ftpmaster.internal/ubuntu eoan/main s390x libubsan1 s390x 9.2.1-8ubuntu1 [123 kB] Get:19 http://ftpmaster.internal/ubuntu eoan/main s390x g++-9 s390x 9.2.1-8ubuntu1 [8327 kB] Get:20 http://ftpmaster.internal/ubuntu eoan/main s390x libstdc++-9-dev s390x 9.2.1-8ubuntu1 [1665 kB] Get:21 http://ftpmaster.internal/ubuntu eoan/main s390x libgcc-9-dev s390x 9.2.1-8ubuntu1 [691 kB] Get:22 http://ftpmaster.internal/ubuntu eoan/main s390x gcc-9 s390x 9.2.1-8ubuntu1 [7890 kB] Get:23 http://ftpmaster.internal/ubuntu eoan/main s390x cpp-9 s390x 9.2.1-8ubuntu1 [7146 kB] Get:24 http://ftpmaster.internal/ubuntu eoan/main s390x libstdc++6 s390x 9.2.1-8ubuntu1 [498 kB] Get:25 http://ftpmaster.internal/ubuntu eoan/main s390x libisl21 s390x 0.21-2 [529 kB] Get:26 http://ftpmaster.internal/ubuntu eoan/main s390x libc6 s390x 2.30-0ubuntu1 [2264 kB] Get:27 http://ftpmaster.internal/ubuntu eoan/main s390x libc-bin s390x 2.30-0ubuntu1 [539 kB] Get:28 http://ftpmaster.internal/ubuntu eoan/main s390x libext2fs2 s390x 1.45.3-4ubuntu1 [176 kB] Get:29 http://ftpmaster.internal/ubuntu eoan/main s390x e2fsprogs s390x 1.45.3-4ubuntu1 [502 kB] Get:30 http://ftpmaster.internal/ubuntu eoan/main s390x logsave s390x 1.45.3-4ubuntu1 [9444 B] Get:31 http://ftpmaster.internal/ubuntu eoan/main s390x passwd s390x 1:4.5-1.1ubuntu4 [796 kB] Get:32 http://ftpmaster.internal/ubuntu eoan/main s390x libgnutls30 s390x 3.6.9-4build1 [682 kB] Get:33 http://ftpmaster.internal/ubuntu eoan/main s390x libcom-err2 s390x 1.45.3-4ubuntu1 [8736 B] Get:34 http://ftpmaster.internal/ubuntu eoan/main s390x libss2 s390x 1.45.3-4ubuntu1 [10.6 kB] Get:35 http://ftpmaster.internal/ubuntu eoan/main s390x libapparmor1 s390x 2.13.3-5ubuntu1 [33.7 kB] Get:36 http://ftpmaster.internal/ubuntu eoan/main s390x libdevmapper1.02.1 s390x 2:1.02.155-2ubuntu6 [122 kB] Get:37 http://ftpmaster.internal/ubuntu eoan/main s390x libsqlite3-0 s390x 3.29.0-2 [497 kB] Get:38 http://ftpmaster.internal/ubuntu eoan/main s390x g++ s390x 4:9.2.1-3.1ubuntu1 [1608 B] Get:39 http://ftpmaster.internal/ubuntu eoan/main s390x gcc s390x 4:9.2.1-3.1ubuntu1 [5208 B] Get:40 http://ftpmaster.internal/ubuntu eoan/main s390x cpp s390x 4:9.2.1-3.1ubuntu1 [27.6 kB] Get:41 http://ftpmaster.internal/ubuntu eoan/main s390x dpkg-dev all 1.19.7ubuntu2 [679 kB] Get:42 http://ftpmaster.internal/ubuntu eoan/main s390x libdpkg-perl all 1.19.7ubuntu2 [230 kB] Get:43 http://ftpmaster.internal/ubuntu eoan/main s390x build-essential s390x 12.7ubuntu1 [4648 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 41.7 MB in 0s (86.5 MB/s) (Reading database ... 12518 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-3ubuntu2_s390x.deb ... Unpacking coreutils (8.30-3ubuntu2) over (8.30-3ubuntu1) ... Setting up coreutils (8.30-3ubuntu2) ... (Reading database ... 12518 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.7ubuntu2_s390x.deb ... Unpacking dpkg (1.19.7ubuntu2) over (1.19.7ubuntu1) ... Setting up dpkg (1.19.7ubuntu2) ... (Reading database ... 12518 files and directories currently installed.) Preparing to unpack .../login_1%3a4.5-1.1ubuntu4_s390x.deb ... Unpacking login (1:4.5-1.1ubuntu4) over (1:4.5-1.1ubuntu3) ... Setting up login (1:4.5-1.1ubuntu4) ... (Reading database ... 12518 files and directories currently installed.) Preparing to unpack .../0-libc6-dev_2.30-0ubuntu1_s390x.deb ... Unpacking libc6-dev:s390x (2.30-0ubuntu1) over (2.29-0ubuntu3) ... Preparing to unpack .../1-libc-dev-bin_2.30-0ubuntu1_s390x.deb ... Unpacking libc-dev-bin (2.30-0ubuntu1) over (2.29-0ubuntu3) ... Preparing to unpack .../2-linux-libc-dev_5.3.0-10.11_s390x.deb ... Unpacking linux-libc-dev:s390x (5.3.0-10.11) over (5.2.0-15.16) ... Preparing to unpack .../3-libcc1-0_9.2.1-8ubuntu1_s390x.deb ... Unpacking libcc1-0:s390x (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../4-binutils-s390x-linux-gnu_2.32.51.20190905-0ubuntu1_s390x.deb ... Unpacking binutils-s390x-linux-gnu (2.32.51.20190905-0ubuntu1) over (2.32.51.20190821-1ubuntu1) ... Preparing to unpack .../5-libbinutils_2.32.51.20190905-0ubuntu1_s390x.deb ... Unpacking libbinutils:s390x (2.32.51.20190905-0ubuntu1) over (2.32.51.20190821-1ubuntu1) ... Preparing to unpack .../6-binutils-common_2.32.51.20190905-0ubuntu1_s390x.deb ... Unpacking binutils-common:s390x (2.32.51.20190905-0ubuntu1) over (2.32.51.20190821-1ubuntu1) ... Preparing to unpack .../7-binutils_2.32.51.20190905-0ubuntu1_s390x.deb ... Unpacking binutils (2.32.51.20190905-0ubuntu1) over (2.32.51.20190821-1ubuntu1) ... 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Unpacking libasan5:s390x (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../04-libubsan1_9.2.1-8ubuntu1_s390x.deb ... Unpacking libubsan1:s390x (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../05-g++-9_9.2.1-8ubuntu1_s390x.deb ... Unpacking g++-9 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../06-libstdc++-9-dev_9.2.1-8ubuntu1_s390x.deb ... Unpacking libstdc++-9-dev:s390x (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../07-libgcc-9-dev_9.2.1-8ubuntu1_s390x.deb ... Unpacking libgcc-9-dev:s390x (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../08-gcc-9_9.2.1-8ubuntu1_s390x.deb ... Unpacking gcc-9 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../09-cpp-9_9.2.1-8ubuntu1_s390x.deb ... Unpacking cpp-9 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../10-libstdc++6_9.2.1-8ubuntu1_s390x.deb ... Unpacking libstdc++6:s390x (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Setting up libstdc++6:s390x (9.2.1-8ubuntu1) ... (Reading database ... 12529 files and directories currently installed.) Preparing to unpack .../libisl21_0.21-2_s390x.deb ... Unpacking libisl21:s390x (0.21-2) over (0.21-1) ... Preparing to unpack .../libc6_2.30-0ubuntu1_s390x.deb ... Unpacking libc6:s390x (2.30-0ubuntu1) over (2.29-0ubuntu3) ... Setting up libc6:s390x (2.30-0ubuntu1) ... (Reading database ... 12529 files and directories currently installed.) Preparing to unpack .../libc-bin_2.30-0ubuntu1_s390x.deb ... Unpacking libc-bin (2.30-0ubuntu1) over (2.29-0ubuntu3) ... Setting up libc-bin (2.30-0ubuntu1) ... (Reading database ... 12529 files and directories currently installed.) Preparing to unpack .../libext2fs2_1.45.3-4ubuntu1_s390x.deb ... Unpacking libext2fs2:s390x (1.45.3-4ubuntu1) over (1.45.2-1ubuntu1) ... Setting up libext2fs2:s390x (1.45.3-4ubuntu1) ... (Reading database ... 12529 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.45.3-4ubuntu1_s390x.deb ... Unpacking e2fsprogs (1.45.3-4ubuntu1) over (1.45.2-1ubuntu1) ... Selecting previously unselected package logsave. Preparing to unpack .../logsave_1.45.3-4ubuntu1_s390x.deb ... Unpacking logsave (1.45.3-4ubuntu1) ... Preparing to unpack .../passwd_1%3a4.5-1.1ubuntu4_s390x.deb ... Unpacking passwd (1:4.5-1.1ubuntu4) over (1:4.5-1.1ubuntu3) ... Setting up passwd (1:4.5-1.1ubuntu4) ... (Reading database ... 12532 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.9-4build1_s390x.deb ... Unpacking libgnutls30:s390x (3.6.9-4build1) over (3.6.9-4) ... Setting up libgnutls30:s390x (3.6.9-4build1) ... (Reading database ... 12532 files and directories currently installed.) Preparing to unpack .../00-libcom-err2_1.45.3-4ubuntu1_s390x.deb ... Unpacking libcom-err2:s390x (1.45.3-4ubuntu1) over (1.45.2-1ubuntu1) ... Preparing to unpack .../01-libss2_1.45.3-4ubuntu1_s390x.deb ... Unpacking libss2:s390x (1.45.3-4ubuntu1) over (1.45.2-1ubuntu1) ... Preparing to unpack .../02-libapparmor1_2.13.3-5ubuntu1_s390x.deb ... Unpacking libapparmor1:s390x (2.13.3-5ubuntu1) over (2.13.2-9ubuntu7) ... Preparing to unpack .../03-libdevmapper1.02.1_2%3a1.02.155-2ubuntu6_s390x.deb ... Unpacking libdevmapper1.02.1:s390x (2:1.02.155-2ubuntu6) over (2:1.02.155-2ubuntu5) ... Preparing to unpack .../04-libsqlite3-0_3.29.0-2_s390x.deb ... Unpacking libsqlite3-0:s390x (3.29.0-2) over (3.29.0-1) ... Preparing to unpack .../05-g++_4%3a9.2.1-3.1ubuntu1_s390x.deb ... Unpacking g++ (4:9.2.1-3.1ubuntu1) over (4:9.2.1-2ubuntu2) ... Preparing to unpack .../06-gcc_4%3a9.2.1-3.1ubuntu1_s390x.deb ... Unpacking gcc (4:9.2.1-3.1ubuntu1) over (4:9.2.1-2ubuntu2) ... Preparing to unpack .../07-cpp_4%3a9.2.1-3.1ubuntu1_s390x.deb ... Unpacking cpp (4:9.2.1-3.1ubuntu1) over (4:9.2.1-2ubuntu2) ... Preparing to unpack .../08-dpkg-dev_1.19.7ubuntu2_all.deb ... Unpacking dpkg-dev (1.19.7ubuntu2) over (1.19.7ubuntu1) ... Preparing to unpack .../09-libdpkg-perl_1.19.7ubuntu2_all.deb ... Unpacking libdpkg-perl (1.19.7ubuntu2) over (1.19.7ubuntu1) ... Preparing to unpack .../10-build-essential_12.7ubuntu1_s390x.deb ... Unpacking build-essential (12.7ubuntu1) over (12.6ubuntu2) ... Setting up libisl21:s390x (0.21-2) ... Setting up libapparmor1:s390x (2.13.3-5ubuntu1) ... Setting up libsqlite3-0:s390x (3.29.0-2) ... Setting up binutils-common:s390x (2.32.51.20190905-0ubuntu1) ... Setting up linux-libc-dev:s390x (5.3.0-10.11) ... Setting up libcom-err2:s390x (1.45.3-4ubuntu1) ... Setting up libgomp1:s390x (9.2.1-8ubuntu1) ... Setting up libasan5:s390x (9.2.1-8ubuntu1) ... Setting up libatomic1:s390x (9.2.1-8ubuntu1) ... Setting up libss2:s390x (1.45.3-4ubuntu1) ... Setting up libdpkg-perl (1.19.7ubuntu2) ... Setting up logsave (1.45.3-4ubuntu1) ... Setting up libubsan1:s390x (9.2.1-8ubuntu1) ... Setting up libdevmapper1.02.1:s390x (2:1.02.155-2ubuntu6) ... Setting up cpp-9 (9.2.1-8ubuntu1) ... Setting up libbinutils:s390x (2.32.51.20190905-0ubuntu1) ... Setting up libc-dev-bin (2.30-0ubuntu1) ... Setting up libcc1-0:s390x (9.2.1-8ubuntu1) ... Setting up libitm1:s390x (9.2.1-8ubuntu1) ... Setting up binutils-s390x-linux-gnu (2.32.51.20190905-0ubuntu1) ... Setting up e2fsprogs (1.45.3-4ubuntu1) ... Installing new version of config file /etc/cron.d/e2scrub_all ... Installing new version of config file /etc/e2scrub.conf ... Setting up binutils (2.32.51.20190905-0ubuntu1) ... Setting up dpkg-dev (1.19.7ubuntu2) ... Setting up libgcc-9-dev:s390x (9.2.1-8ubuntu1) ... Setting up cpp (4:9.2.1-3.1ubuntu1) ... Setting up libc6-dev:s390x (2.30-0ubuntu1) ... Setting up gcc-9 (9.2.1-8ubuntu1) ... Setting up libstdc++-9-dev:s390x (9.2.1-8ubuntu1) ... Setting up gcc (4:9.2.1-3.1ubuntu1) ... Setting up g++-9 (9.2.1-8ubuntu1) ... Setting up g++ (4:9.2.1-3.1ubuntu1) ... Setting up build-essential (12.7ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-17534378 s390x eoan -c chroot:build-PACKAGEBUILD-17534378 --arch=s390x --dist=eoan --nolog bcftools_1.9-1.dsc Initiating build PACKAGEBUILD-17534378 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-161-generic #189-Ubuntu SMP Tue Aug 27 08:09:43 UTC 2019 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-s390x-008.buildd +==============================================================================+ | bcftools 1.9-1 (s390x) 14 Sep 2019 17:21 | +==============================================================================+ Package: bcftools Version: 1.9-1 Source Version: 1.9-1 Distribution: eoan Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/bcftools-fpUNkD/bcftools-1.9' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-fpUNkD' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-17534378/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-F0YSHD/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-F0YSHD/apt_archive ./ InRelease Get:2 copy:/<>/resolver-F0YSHD/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-F0YSHD/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-F0YSHD/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-F0YSHD/apt_archive ./ Packages [526 B] Fetched 2859 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 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 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-F0YSHD/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12532 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-NjMXqD/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. Ign:1 copy:/<>/resolver-NjMXqD/apt_archive ./ InRelease Get:2 copy:/<>/resolver-NjMXqD/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-NjMXqD/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-NjMXqD/apt_archive ./ Sources [271 B] Get:5 copy:/<>/resolver-NjMXqD/apt_archive ./ Packages [578 B] Fetched 2968 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 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 libsub-override-perl 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 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 25.5 MB of archives. After this operation, 91.7 MB of additional disk space will be used. Get:1 copy:/<>/resolver-NjMXqD/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [904 B] Get:2 http://ftpmaster.internal/ubuntu eoan/main s390x libbsd0 s390x 0.10.0-1 [43.7 kB] Get:3 http://ftpmaster.internal/ubuntu eoan/main s390x bsdmainutils s390x 11.1.2ubuntu2 [181 kB] Get:4 http://ftpmaster.internal/ubuntu eoan/main s390x libuchardet0 s390x 0.0.6-3 [64.5 kB] Get:5 http://ftpmaster.internal/ubuntu eoan/main s390x groff-base s390x 1.22.4-3 [819 kB] Get:6 http://ftpmaster.internal/ubuntu eoan/main s390x libpipeline1 s390x 1.5.1-2 [24.5 kB] Get:7 http://ftpmaster.internal/ubuntu eoan/main s390x man-db s390x 2.8.7-3 [1099 kB] Get:8 http://ftpmaster.internal/ubuntu eoan/main s390x libmagic-mgc s390x 1:5.37-5 [210 kB] Get:9 http://ftpmaster.internal/ubuntu eoan/main s390x libmagic1 s390x 1:5.37-5 [72.0 kB] Get:10 http://ftpmaster.internal/ubuntu eoan/main s390x file s390x 1:5.37-5 [22.9 kB] Get:11 http://ftpmaster.internal/ubuntu eoan/main s390x libelf1 s390x 0.176-1.1 [41.4 kB] Get:12 http://ftpmaster.internal/ubuntu eoan/main s390x libglib2.0-0 s390x 2.62.0-1 [1159 kB] Get:13 http://ftpmaster.internal/ubuntu eoan/main s390x libicu63 s390x 63.2-2 [8044 kB] Get:14 http://ftpmaster.internal/ubuntu eoan/main s390x libxml2 s390x 2.9.4+dfsg1-7ubuntu3 [553 kB] Get:15 http://ftpmaster.internal/ubuntu eoan/main s390x gettext-base s390x 0.19.8.1-9 [48.1 kB] Get:16 http://ftpmaster.internal/ubuntu eoan/main s390x libkrb5support0 s390x 1.17-6 [30.4 kB] Get:17 http://ftpmaster.internal/ubuntu eoan/main s390x libk5crypto3 s390x 1.17-6 [77.9 kB] Get:18 http://ftpmaster.internal/ubuntu eoan/main s390x libkeyutils1 s390x 1.6-6 [9816 B] Get:19 http://ftpmaster.internal/ubuntu eoan/main s390x libkrb5-3 s390x 1.17-6 [308 kB] Get:20 http://ftpmaster.internal/ubuntu eoan/main s390x libgssapi-krb5-2 s390x 1.17-6 [110 kB] Get:21 http://ftpmaster.internal/ubuntu eoan/main s390x libpsl5 s390x 0.20.2-2 [49.8 kB] Get:22 http://ftpmaster.internal/ubuntu eoan/main s390x libsigsegv2 s390x 2.12-2 [13.8 kB] Get:23 http://ftpmaster.internal/ubuntu eoan/main s390x m4 s390x 1.4.18-2 [194 kB] Get:24 http://ftpmaster.internal/ubuntu eoan/main s390x autoconf all 2.69-11 [322 kB] Get:25 http://ftpmaster.internal/ubuntu eoan/main s390x autotools-dev all 20180224.1 [39.6 kB] Get:26 http://ftpmaster.internal/ubuntu eoan/main s390x automake all 1:1.16.1-4ubuntu3 [522 kB] Get:27 http://ftpmaster.internal/ubuntu eoan/main s390x autopoint all 0.19.8.1-9 [412 kB] Get:28 http://ftpmaster.internal/ubuntu eoan/main s390x libtool all 2.4.6-11 [194 kB] Get:29 http://ftpmaster.internal/ubuntu eoan/main s390x dh-autoreconf all 19 [16.1 kB] Get:30 http://ftpmaster.internal/ubuntu eoan/main s390x libarchive-zip-perl all 1.65-1 [83.6 kB] Get:31 http://ftpmaster.internal/ubuntu eoan/main s390x libsub-override-perl all 0.09-2 [9532 B] Get:32 http://ftpmaster.internal/ubuntu eoan/main s390x libfile-stripnondeterminism-perl all 1.6.0-1 [16.2 kB] Get:33 http://ftpmaster.internal/ubuntu eoan/main s390x dh-strip-nondeterminism all 1.6.0-1 [5208 B] Get:34 http://ftpmaster.internal/ubuntu eoan/main s390x dwz s390x 0.13-1 [75.0 kB] Get:35 http://ftpmaster.internal/ubuntu eoan/main s390x libcroco3 s390x 0.6.13-1 [73.7 kB] Get:36 http://ftpmaster.internal/ubuntu eoan/main s390x gettext s390x 0.19.8.1-9 [858 kB] Get:37 http://ftpmaster.internal/ubuntu eoan/main s390x intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:38 http://ftpmaster.internal/ubuntu eoan/main s390x po-debconf all 1.0.21 [233 kB] Get:39 http://ftpmaster.internal/ubuntu eoan/main s390x debhelper all 12.4ubuntu1 [910 kB] Get:40 http://ftpmaster.internal/ubuntu eoan/main s390x libroken18-heimdal s390x 7.5.0+dfsg-3build1 [39.4 kB] Get:41 http://ftpmaster.internal/ubuntu eoan/main s390x libasn1-8-heimdal s390x 7.5.0+dfsg-3build1 [148 kB] Get:42 http://ftpmaster.internal/ubuntu eoan/main s390x libbz2-dev s390x 1.0.6-9.2 [30.3 kB] Get:43 http://ftpmaster.internal/ubuntu eoan/main s390x libheimbase1-heimdal s390x 7.5.0+dfsg-3build1 [27.4 kB] Get:44 http://ftpmaster.internal/ubuntu eoan/main s390x libhcrypto4-heimdal s390x 7.5.0+dfsg-3build1 [82.4 kB] Get:45 http://ftpmaster.internal/ubuntu eoan/main s390x libwind0-heimdal s390x 7.5.0+dfsg-3build1 [47.7 kB] Get:46 http://ftpmaster.internal/ubuntu eoan/main s390x libhx509-5-heimdal s390x 7.5.0+dfsg-3build1 [97.6 kB] Get:47 http://ftpmaster.internal/ubuntu eoan/main s390x libkrb5-26-heimdal s390x 7.5.0+dfsg-3build1 [189 kB] Get:48 http://ftpmaster.internal/ubuntu eoan/main s390x libheimntlm0-heimdal s390x 7.5.0+dfsg-3build1 [14.1 kB] Get:49 http://ftpmaster.internal/ubuntu eoan/main s390x libgssapi3-heimdal s390x 7.5.0+dfsg-3build1 [86.5 kB] Get:50 http://ftpmaster.internal/ubuntu eoan/main s390x libsasl2-modules-db s390x 2.1.27+dfsg-1build3 [13.7 kB] Get:51 http://ftpmaster.internal/ubuntu eoan/main s390x libsasl2-2 s390x 2.1.27+dfsg-1build3 [46.3 kB] Get:52 http://ftpmaster.internal/ubuntu eoan/main s390x libldap-common all 2.4.48+dfsg-1ubuntu1 [17.3 kB] Get:53 http://ftpmaster.internal/ubuntu eoan/main s390x libldap-2.4-2 s390x 2.4.48+dfsg-1ubuntu1 [144 kB] Get:54 http://ftpmaster.internal/ubuntu eoan/main s390x libnghttp2-14 s390x 1.39.2-1 [74.7 kB] Get:55 http://ftpmaster.internal/ubuntu eoan/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2 [51.1 kB] Get:56 http://ftpmaster.internal/ubuntu eoan/main s390x libssh-4 s390x 0.9.0-1 [180 kB] Get:57 http://ftpmaster.internal/ubuntu eoan/main s390x libcurl3-gnutls s390x 7.65.3-1ubuntu2 [210 kB] Get:58 http://ftpmaster.internal/ubuntu eoan/universe s390x libdeflate0 s390x 1.2-1 [52.4 kB] Get:59 http://ftpmaster.internal/ubuntu eoan/universe s390x libgslcblas0 s390x 2.5+dfsg-6 [72.7 kB] Get:60 http://ftpmaster.internal/ubuntu eoan/universe s390x libgsl23 s390x 2.5+dfsg-6 [747 kB] Get:61 http://ftpmaster.internal/ubuntu eoan/universe s390x libgsl-dev s390x 2.5+dfsg-6 [934 kB] Get:62 http://ftpmaster.internal/ubuntu eoan/universe s390x libhts2 s390x 1.9-10 [268 kB] Get:63 http://ftpmaster.internal/ubuntu eoan/main s390x liblzma-dev s390x 5.2.4-1 [145 kB] Get:64 http://ftpmaster.internal/ubuntu eoan/main s390x zlib1g-dev s390x 1:1.2.11.dfsg-1ubuntu3 [173 kB] Get:65 http://ftpmaster.internal/ubuntu eoan/universe s390x libhts-dev s390x 1.9-10 [4334 kB] Get:66 http://ftpmaster.internal/ubuntu eoan/main s390x libio-pty-perl s390x 1:1.08-1.1build6 [29.3 kB] Get:67 http://ftpmaster.internal/ubuntu eoan/universe s390x tabix s390x 1.9-10 [253 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.5 MB in 0s (71.1 MB/s) Selecting previously unselected package libbsd0:s390x. 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Unpacking libgslcblas0:s390x (2.5+dfsg-6) ... Selecting previously unselected package libgsl23:s390x. Preparing to unpack .../58-libgsl23_2.5+dfsg-6_s390x.deb ... Unpacking libgsl23:s390x (2.5+dfsg-6) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../59-libgsl-dev_2.5+dfsg-6_s390x.deb ... Unpacking libgsl-dev (2.5+dfsg-6) ... Selecting previously unselected package libhts2:s390x. Preparing to unpack .../60-libhts2_1.9-10_s390x.deb ... Unpacking libhts2:s390x (1.9-10) ... Selecting previously unselected package liblzma-dev:s390x. Preparing to unpack .../61-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 .../62-zlib1g-dev_1%3a1.2.11.dfsg-1ubuntu3_s390x.deb ... Unpacking zlib1g-dev:s390x (1:1.2.11.dfsg-1ubuntu3) ... Selecting previously unselected package libhts-dev:s390x. Preparing to unpack .../63-libhts-dev_1.9-10_s390x.deb ... Unpacking libhts-dev:s390x (1.9-10) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../64-libio-pty-perl_1%3a1.08-1.1build6_s390x.deb ... Unpacking libio-pty-perl (1:1.08-1.1build6) ... Selecting previously unselected package tabix. Preparing to unpack .../65-tabix_1.9-10_s390x.deb ... Unpacking tabix (1.9-10) ... Selecting previously unselected package sbuild-build-depends-bcftools-dummy. Preparing to unpack .../66-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 (1:1.08-1.1build6) ... Setting up libmagic-mgc (1:5.37-5) ... Setting up libarchive-zip-perl (1.65-1) ... Setting up libglib2.0-0:s390x (2.62.0-1) ... No schema files found: doing nothing. Setting up libnghttp2-14:s390x (1.39.2-1) ... Setting up libmagic1:s390x (1:5.37-5) ... Setting up libdeflate0:s390x (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.37-5) ... Setting up libldap-common (2.4.48+dfsg-1ubuntu1) ... Setting up libicu63:s390x (63.2-2) ... Setting up libkrb5support0:s390x (1.17-6) ... Setting up libsasl2-modules-db:s390x (2.1.27+dfsg-1build3) ... 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 (1.17-6) ... Setting up libsasl2-2:s390x (2.1.27+dfsg-1build3) ... Setting up libroken18-heimdal:s390x (7.5.0+dfsg-3build1) ... Setting up liblzma-dev:s390x (5.2.4-1) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-1ubuntu3) ... Setting up libuchardet0:s390x (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:s390x (1.17-6) ... Setting up libbsd0:s390x (0.10.0-1) ... Setting up libelf1:s390x (0.176-1.1) ... Setting up libxml2:s390x (2.9.4+dfsg1-7ubuntu3) ... Setting up libheimbase1-heimdal:s390x (7.5.0+dfsg-3build1) ... Setting up libbz2-dev:s390x (1.0.6-9.2) ... Setting up libfile-stripnondeterminism-perl (1.6.0-1) ... Setting up libgsl-dev (2.5+dfsg-6) ... Setting up libtool (2.4.6-11) ... Setting up libasn1-8-heimdal:s390x (7.5.0+dfsg-3build1) ... Setting up m4 (1.4.18-2) ... Setting up libhcrypto4-heimdal:s390x (7.5.0+dfsg-3build1) ... Setting up libwind0-heimdal:s390x (7.5.0+dfsg-3build1) ... 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 (1.17-6) ... Setting up libcroco3:s390x (0.6.13-1) ... Setting up libssh-4:s390x (0.9.0-1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.13-1) ... 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-3build1) ... Setting up man-db (2.8.7-3) ... 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-3build1) ... Setting up po-debconf (1.0.21) ... Setting up libheimntlm0-heimdal:s390x (7.5.0+dfsg-3build1) ... Setting up libgssapi3-heimdal:s390x (7.5.0+dfsg-3build1) ... Setting up libldap-2.4-2:s390x (2.4.48+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:s390x (7.65.3-1ubuntu2) ... Setting up tabix (1.9-10) ... Setting up libhts2:s390x (1.9-10) ... Setting up libhts-dev:s390x (1.9-10) ... Setting up debhelper (12.4ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.6.0-1) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-161-generic s390x (s390x) Toolchain package versions: binutils_2.32.51.20190905-0ubuntu1 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-8ubuntu1 gcc-9_9.2.1-8ubuntu1 libc6-dev_2.30-0ubuntu1 libstdc++-9-dev_9.2.1-8ubuntu1 libstdc++6_9.2.1-8ubuntu1 linux-libc-dev_5.3.0-10.11 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.3 autoconf_2.69-11 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.2ubuntu6 base-passwd_3.5.46 bash_5.0-4ubuntu1 binutils_2.32.51.20190905-0ubuntu1 binutils-common_2.32.51.20190905-0ubuntu1 binutils-s390x-linux-gnu_2.32.51.20190905-0ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu2 build-essential_12.7ubuntu1 bzip2_1.0.6-9.2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-8ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.4ubuntu1 debianutils_4.8.6.3 dh-autoreconf_19 dh-strip-nondeterminism_1.6.0-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu2 dpkg-dev_1.19.7ubuntu2 dwz_0.13-1 e2fsprogs_1.45.3-4ubuntu1 fakeroot_1.23-1 fdisk_2.34-0.1ubuntu2 file_1:5.37-5 findutils_4.6.0+git+20190209-2ubuntu1 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-8ubuntu1 gcc_4:9.2.1-3.1ubuntu1 gcc-9_9.2.1-8ubuntu1 gcc-9-base_9.2.1-8ubuntu1 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_1.10-0ubuntu3 hostname_3.22 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapparmor1_2.13.3-5ubuntu1 libapt-pkg5.90_1.9.3 libarchive-zip-perl_1.65-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-8ubuntu1 libasn1-8-heimdal_7.5.0+dfsg-3build1 libassuan0_2.5.3-7ubuntu1 libatomic1_9.2.1-8ubuntu1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.5-2ubuntu1 libaudit1_1:2.8.5-2ubuntu1 libbinutils_2.32.51.20190905-0ubuntu1 libblkid1_2.34-0.1ubuntu2 libbsd0_0.10.0-1 libbz2-1.0_1.0.6-9.2 libbz2-dev_1.0.6-9.2 libc-bin_2.30-0ubuntu1 libc-dev-bin_2.30-0ubuntu1 libc6_2.30-0ubuntu1 libc6-dev_2.30-0ubuntu1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_9.2.1-8ubuntu1 libcom-err2_1.45.3-4ubuntu1 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.0-3ubuntu1 libcurl3-gnutls_7.65.3-1ubuntu2 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.249ubuntu1 libdeflate0_1.2-1 libdevmapper1.02.1_2:1.02.155-2ubuntu6 libdpkg-perl_1.19.7ubuntu2 libelf1_0.176-1.1 libext2fs2_1.45.3-4ubuntu1 libfakeroot_1.23-1 libfdisk1_2.34-0.1ubuntu2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.0-1 libgcc-9-dev_9.2.1-8ubuntu1 libgcc1_1:9.2.1-8ubuntu1 libgcrypt20_1.8.4-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.0-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-4build1 libgomp1_9.2.1-8ubuntu1 libgpg-error0_1.36-7 libgsl-dev_2.5+dfsg-6 libgsl23_2.5+dfsg-6 libgslcblas0_2.5+dfsg-6 libgssapi-krb5-2_1.17-6 libgssapi3-heimdal_7.5.0+dfsg-3build1 libhcrypto4-heimdal_7.5.0+dfsg-3build1 libheimbase1-heimdal_7.5.0+dfsg-3build1 libheimntlm0-heimdal_7.5.0+dfsg-3build1 libhogweed4_3.4.1-1 libhts-dev_1.9-10 libhts2_1.9-10 libhx509-5-heimdal_7.5.0+dfsg-3build1 libicu63_63.2-2 libidn11_1.33-2.2ubuntu2 libidn2-0_2.2.0-1 libio-pty-perl_1:1.08-1.1build6 libip4tc2_1.8.3-2ubuntu2 libisl21_0.21-2 libitm1_9.2.1-8ubuntu1 libjson-c4_0.13.1+dfsg-4 libk5crypto3_1.17-6 libkeyutils1_1.6-6 libkmod2_26-1ubuntu1 libkrb5-26-heimdal_7.5.0+dfsg-3build1 libkrb5-3_1.17-6 libkrb5support0_1.17-6 libldap-2.4-2_2.4.48+dfsg-1ubuntu1 libldap-common_2.4.48+dfsg-1ubuntu1 liblockfile-bin_1.15-1 liblockfile1_1.15-1 liblz4-1_1.9.1-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.34-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.1+20190803-1ubuntu1 libncursesw6_6.1+20190803-1ubuntu1 libnettle6_3.4.1-1 libnghttp2-14_1.39.2-1 libnpth0_1.6-1 libp11-kit0_0.23.16.1-2 libpam-modules_1.3.1-5ubuntu1 libpam-modules-bin_1.3.1-5ubuntu1 libpam-runtime_1.3.1-5ubuntu1 libpam0g_1.3.1-5ubuntu1 libpcre2-8-0_10.32-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpng16-16_1.6.37-1 libprocps7_2:3.3.15-2ubuntu3 libpsl5_0.20.2-2 libreadline8_8.0-3 libroken18-heimdal_7.5.0+dfsg-3build1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1build3 libsasl2-modules-db_2.1.27+dfsg-1build3 libseccomp2_2.4.1-0ubuntu0.19.10.3 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu2 libsqlite3-0_3.29.0-2 libss2_1.45.3-4ubuntu1 libssh-4_0.9.0-1 libssl1.1_1.1.1c-1ubuntu4 libstdc++-9-dev_9.2.1-8ubuntu1 libstdc++6_9.2.1-8ubuntu1 libsub-override-perl_0.09-2 libsystemd0_241-7ubuntu1 libtasn1-6_4.14-2 libtinfo6_6.1+20190803-1ubuntu1 libtool_2.4.6-11 libubsan1_9.2.1-8ubuntu1 libuchardet0_0.0.6-3 libudev1_241-7ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu2 libwind0-heimdal_7.5.0+dfsg-3build1 libxml2_2.9.4+dfsg1-7ubuntu3 libzstd1_1.4.3+dfsg-1 linux-libc-dev_5.3.0-10.11 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu4 logsave_1.45.3-4ubuntu1 lsb-base_11.0.1ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.7-3 mawk_1.3.3-17ubuntu3 mount_2.34-0.1ubuntu2 ncurses-base_6.1+20190803-1ubuntu1 ncurses-bin_6.1+20190803-1ubuntu1 openssl_1.1.1c-1ubuntu4 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu4 patch_2.7.6-6 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 readline-common_8.0-3 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_241-7ubuntu1 systemd-sysv_241-7ubuntu1 sysvinit-utils_2.95-5ubuntu2 tabix_1.9-10 tar_1.30+dfsg-6 tzdata_2019b-2 ubuntu-keyring_2018.09.18.1 util-linux_2.34-0.1ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | 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=noautodbgsym 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-17534378 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-17534378 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-17534378 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 vcfmerge.c: In function ‘maux_init’: vcfmerge.c:682:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 682 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:29, from /usr/include/htslib/vcf.h:40, from vcfmerge.c:31: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ 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 In function ‘realign’, inlined from ‘normalize_line’ at vcfnorm.c:1717:23: vcfnorm.c:345:17: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 345 | error("Non-ACGTN alternate allele at %s:%d .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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=] 2334 | 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 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __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/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/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/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/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/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/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/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/R1uRGzRFMW/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/R1uRGzRFMW/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/R1uRGzRFMW/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/R1uRGzRFMW/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/R1uRGzRFMW/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/R1uRGzRFMW/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/R1uRGzRFMW/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/R1uRGzRFMW/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/R1uRGzRFMW/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/R1uRGzRFMW/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/R1uRGzRFMW/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/R1uRGzRFMW/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/R1uRGzRFMW/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/R1uRGzRFMW/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/R1uRGzRFMW/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/R1uRGzRFMW/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/R1uRGzRFMW/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/R1uRGzRFMW/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/R1uRGzRFMW/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/R1uRGzRFMW/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/R1uRGzRFMW/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/R1uRGzRFMW/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/R1uRGzRFMW/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/R1uRGzRFMW/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/R1uRGzRFMW/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/R1uRGzRFMW/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/R1uRGzRFMW/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/check.1.chk /tmp/R1uRGzRFMW/check.2.chk /tmp/R1uRGzRFMW/check.3.chk /tmp/R1uRGzRFMW/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/R1uRGzRFMW/stats.a.vcf.gz /tmp/R1uRGzRFMW/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/R1uRGzRFMW/stats.a.vcf.gz /tmp/R1uRGzRFMW/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/R1uRGzRFMW/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/R1uRGzRFMW/isec.a.vcf.gz /tmp/R1uRGzRFMW/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/R1uRGzRFMW/isec.a.vcf.gz /tmp/R1uRGzRFMW/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/R1uRGzRFMW/isec.a.vcf.gz /tmp/R1uRGzRFMW/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/R1uRGzRFMW/isec.a.vcf.gz /tmp/R1uRGzRFMW/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/R1uRGzRFMW/isec.a.vcf.gz /tmp/R1uRGzRFMW/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/R1uRGzRFMW/isec.a.vcf.gz /tmp/R1uRGzRFMW/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/R1uRGzRFMW/isec.a.vcf.gz /tmp/R1uRGzRFMW/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/R1uRGzRFMW/isec.a.vcf.gz /tmp/R1uRGzRFMW/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/R1uRGzRFMW/isec.a.vcf.gz /tmp/R1uRGzRFMW/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/R1uRGzRFMW/isec.a.vcf.gz /tmp/R1uRGzRFMW/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/R1uRGzRFMW/isec.tab.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/isec.tab.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.a.vcf.gz /tmp/R1uRGzRFMW/merge.b.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.a.vcf.gz /tmp/R1uRGzRFMW/merge.b.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.a.vcf.gz /tmp/R1uRGzRFMW/merge.b.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.a.vcf.gz /tmp/R1uRGzRFMW/merge.b.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.a.vcf.gz /tmp/R1uRGzRFMW/merge.b.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.a.vcf.gz /tmp/R1uRGzRFMW/merge.b.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.2.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.2.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.2.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.2.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.2.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.2.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.3.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.3.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.4.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.4.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/gvcf.merge.1.vcf.gz /tmp/R1uRGzRFMW/gvcf.merge.2.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/gvcf.merge.1.vcf.gz /tmp/R1uRGzRFMW/gvcf.merge.2.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.gvcf.2.a.vcf.gz /tmp/R1uRGzRFMW/merge.gvcf.2.b.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.gvcf.2.a.vcf.gz /tmp/R1uRGzRFMW/merge.gvcf.2.b.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/merge.gvcf.3.a.vcf.gz /tmp/R1uRGzRFMW/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/R1uRGzRFMW/merge.gvcf.3.a.vcf.gz /tmp/R1uRGzRFMW/merge.gvcf.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/R1uRGzRFMW/merge.5.a.vcf.gz /tmp/R1uRGzRFMW/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/R1uRGzRFMW/merge.5.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.vectors.vcf.gz The outputs differ: /<>/test/query.12.out /<>/test/query.12.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/missing.vcf.gz | /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/R1uRGzRFMW/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/R1uRGzRFMW/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter.4.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/norm.split.vcf.gz 2>/dev/null Non-zero status 1 .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/R1uRGzRFMW/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/R1uRGzRFMW/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/R1uRGzRFMW/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/R1uRGzRFMW/norm.split.vcf.gz 2>/dev/null Non-zero status 255 .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m- -f /<>/test/norm.fa /tmp/R1uRGzRFMW/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/R1uRGzRFMW/norm.merge.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.merge.out /<>/test/norm.merge.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/R1uRGzRFMW/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/R1uRGzRFMW/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/R1uRGzRFMW/norm.merge.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/R1uRGzRFMW/norm.merge.3.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/R1uRGzRFMW/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/R1uRGzRFMW/norm.merge.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.merge.strict.out /<>/test/norm.merge.strict.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ -s /tmp/R1uRGzRFMW/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/R1uRGzRFMW/norm.setref.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/R1uRGzRFMW/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/R1uRGzRFMW/norm.telomere.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/R1uRGzRFMW/norm.telomere.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/R1uRGzRFMW/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d snps /tmp/R1uRGzRFMW/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/R1uRGzRFMW/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d indels /tmp/R1uRGzRFMW/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/R1uRGzRFMW/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d both /tmp/R1uRGzRFMW/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/R1uRGzRFMW/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d all /tmp/R1uRGzRFMW/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/R1uRGzRFMW/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d none /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/view.vcf.gz The outputs differ: /<>/test/view.5.out /<>/test/view.5.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -p /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.vcf.gz The outputs differ: /<>/test/view.6.out /<>/test/view.6.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -P /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/R1uRGzRFMW/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/R1uRGzRFMW/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/R1uRGzRFMW/view.vcf.gz The outputs differ: /<>/test/view.9.out /<>/test/view.9.out.new .. failed ... test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/R1uRGzRFMW/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/R1uRGzRFMW/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/R1uRGzRFMW/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/R1uRGzRFMW/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/R1uRGzRFMW/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/R1uRGzRFMW/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/R1uRGzRFMW/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/R1uRGzRFMW/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/R1uRGzRFMW/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/R1uRGzRFMW/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/R1uRGzRFMW/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/R1uRGzRFMW/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/R1uRGzRFMW/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/R1uRGzRFMW/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/R1uRGzRFMW/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/R1uRGzRFMW/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/R1uRGzRFMW/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/R1uRGzRFMW/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.ybSsIu 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.i6OBZK 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.uuSY4Z 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.N9Fozg Merging 5 temporary files Cleaning Done .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab /tmp/R1uRGzRFMW/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/R1uRGzRFMW/regions.tab.gz /tmp/R1uRGzRFMW/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/R1uRGzRFMW/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/R1uRGzRFMW/regions.tab.gz /tmp/R1uRGzRFMW/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/R1uRGzRFMW/regions.bed /tmp/R1uRGzRFMW/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/R1uRGzRFMW/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/R1uRGzRFMW/regions.bed /tmp/R1uRGzRFMW/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/R1uRGzRFMW/regions.bed.gz /tmp/R1uRGzRFMW/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/R1uRGzRFMW/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/R1uRGzRFMW/regions.bed.gz /tmp/R1uRGzRFMW/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/R1uRGzRFMW/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R1uRGzRFMW/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/R1uRGzRFMW/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R1uRGzRFMW/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/R1uRGzRFMW/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R1uRGzRFMW/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/R1uRGzRFMW/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R1uRGzRFMW/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/R1uRGzRFMW/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R1uRGzRFMW/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/R1uRGzRFMW/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/R1uRGzRFMW/annots4.vcf.gz -c +INFO /tmp/R1uRGzRFMW/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R1uRGzRFMW/annots4.vcf.gz -c +INFO /tmp/R1uRGzRFMW/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/R1uRGzRFMW/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R1uRGzRFMW/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/R1uRGzRFMW/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/R1uRGzRFMW/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R1uRGzRFMW/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/R1uRGzRFMW/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R1uRGzRFMW/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/R1uRGzRFMW/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R1uRGzRFMW/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/R1uRGzRFMW/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R1uRGzRFMW/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/R1uRGzRFMW/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R1uRGzRFMW/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/R1uRGzRFMW/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/R1uRGzRFMW/annots11.vcf.gz -c FMT /tmp/R1uRGzRFMW/annotate11.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/R1uRGzRFMW/annots11.vcf.gz -c FMT /tmp/R1uRGzRFMW/annotate11.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +missing2ref --no-version /tmp/R1uRGzRFMW/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +missing2ref --no-version /tmp/R1uRGzRFMW/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/R1uRGzRFMW/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/R1uRGzRFMW/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-AN-AC --no-version /tmp/R1uRGzRFMW/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +dosage /tmp/R1uRGzRFMW/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +dosage /tmp/R1uRGzRFMW/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixploidy --no-version /tmp/R1uRGzRFMW/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/R1uRGzRFMW/fixploidy.bcf -- -s /<>/test/fixploidy.samples -p /<>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/R1uRGzRFMW/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/R1uRGzRFMW/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/R1uRGzRFMW/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/R1uRGzRFMW/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/R1uRGzRFMW/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/R1uRGzRFMW/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/R1uRGzRFMW/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +trio-switch-rate /tmp/R1uRGzRFMW/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/R1uRGzRFMW/trio.bcf -- -p /<>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +trio-stats /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +af-dist /tmp/R1uRGzRFMW/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixref /tmp/R1uRGzRFMW/fixref.2a.vcf.gz -- -f /<>/test/norm.fa -i /tmp/R1uRGzRFMW/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixref /tmp/R1uRGzRFMW/fixref.2a.bcf -- -f /<>/test/norm.fa -i /tmp/R1uRGzRFMW/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixref /tmp/R1uRGzRFMW/fixref.3.vcf.gz -- -f /<>/test/fixref.3.fa -m top 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixref /tmp/R1uRGzRFMW/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/R1uRGzRFMW/aa.vcf.gz -- -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 ... [E::bcf_record_check] Bad BCF record - shared section malformed or too short test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/mendelian.vcf.gz -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/R1uRGzRFMW/mendelian.bcf -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/R1uRGzRFMW/mendelian.vcf.gz -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/R1uRGzRFMW/mendelian.bcf -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/R1uRGzRFMW/mendelian.vcf.gz -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/R1uRGzRFMW/mendelian.bcf -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +contrast /tmp/R1uRGzRFMW/contrast.vcf.gz -0 a,b -1 c 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +contrast /tmp/R1uRGzRFMW/contrast.bcf -0 a,b -1 c 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/R1uRGzRFMW/concat.1.a.vcf.gz /tmp/R1uRGzRFMW/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/R1uRGzRFMW/concat.1.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.1.a.bcf /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.1.a.bcf /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.2.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.2.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.2.a.bcf /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.2.a.bcf /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.2.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.2.a.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.2.a.bcf /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.2.a.bcf /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.3.a.vcf.gz /tmp/R1uRGzRFMW/concat.3.b.vcf.gz /tmp/R1uRGzRFMW/concat.3.0.vcf.gz /tmp/R1uRGzRFMW/concat.3.c.vcf.gz /tmp/R1uRGzRFMW/concat.3.d.vcf.gz /tmp/R1uRGzRFMW/concat.3.e.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.3.a.vcf.gz /tmp/R1uRGzRFMW/concat.3.b.vcf.gz /tmp/R1uRGzRFMW/concat.3.0.vcf.gz /tmp/R1uRGzRFMW/concat.3.c.vcf.gz /tmp/R1uRGzRFMW/concat.3.d.vcf.gz /tmp/R1uRGzRFMW/concat.3.e.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.3.a.bcf /tmp/R1uRGzRFMW/concat.3.b.bcf /tmp/R1uRGzRFMW/concat.3.0.bcf /tmp/R1uRGzRFMW/concat.3.c.bcf /tmp/R1uRGzRFMW/concat.3.d.bcf /tmp/R1uRGzRFMW/concat.3.e.bcf /tmp/R1uRGzRFMW/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/R1uRGzRFMW/concat.3.a.bcf /tmp/R1uRGzRFMW/concat.3.b.bcf /tmp/R1uRGzRFMW/concat.3.0.bcf /tmp/R1uRGzRFMW/concat.3.c.bcf /tmp/R1uRGzRFMW/concat.3.d.bcf /tmp/R1uRGzRFMW/concat.3.e.bcf /tmp/R1uRGzRFMW/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: 2130058121 The outputs differ: /<>/test/concat.3.bcf.out /<>/test/concat.3.bcf.out.new .. failed ... test_naive_concat: /<>/bcftools concat --naive /tmp/R1uRGzRFMW/naive_concat.0.bcf /tmp/R1uRGzRFMW/naive_concat.1.bcf /tmp/R1uRGzRFMW/naive_concat.2.bcf /tmp/R1uRGzRFMW/naive_concat.3.bcf /tmp/R1uRGzRFMW/naive_concat.4.bcf /tmp/R1uRGzRFMW/naive_concat.5.bcf /tmp/R1uRGzRFMW/naive_concat.6.bcf /tmp/R1uRGzRFMW/naive_concat.7.bcf /tmp/R1uRGzRFMW/naive_concat.8.bcf /tmp/R1uRGzRFMW/naive_concat.9.bcf | /<>/bcftools view -H [E::hts_realloc_or_die] Cannot allocate memory Failed to open -: unknown file type Non-zero status 255 .. failed ... test_naive_concat: /<>/bcftools concat --naive /tmp/R1uRGzRFMW/naive_concat.0.vcf.gz /tmp/R1uRGzRFMW/naive_concat.1.vcf.gz /tmp/R1uRGzRFMW/naive_concat.2.vcf.gz /tmp/R1uRGzRFMW/naive_concat.3.vcf.gz /tmp/R1uRGzRFMW/naive_concat.4.vcf.gz /tmp/R1uRGzRFMW/naive_concat.5.vcf.gz /tmp/R1uRGzRFMW/naive_concat.6.vcf.gz /tmp/R1uRGzRFMW/naive_concat.7.vcf.gz /tmp/R1uRGzRFMW/naive_concat.8.vcf.gz /tmp/R1uRGzRFMW/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/R1uRGzRFMW/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R1uRGzRFMW/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/R1uRGzRFMW/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R1uRGzRFMW/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/R1uRGzRFMW/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R1uRGzRFMW/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/R1uRGzRFMW/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R1uRGzRFMW/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/R1uRGzRFMW/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R1uRGzRFMW/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/R1uRGzRFMW/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R1uRGzRFMW/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/R1uRGzRFMW/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R1uRGzRFMW/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/R1uRGzRFMW/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R1uRGzRFMW/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/R1uRGzRFMW/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R1uRGzRFMW/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/R1uRGzRFMW/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R1uRGzRFMW/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/R1uRGzRFMW/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R1uRGzRFMW/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/R1uRGzRFMW/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/R1uRGzRFMW/empty.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/R1uRGzRFMW/rename.map -Ov /tmp/R1uRGzRFMW/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/R1uRGzRFMW/rename.map -Ob /tmp/R1uRGzRFMW/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/R1uRGzRFMW/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/R1uRGzRFMW/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/R1uRGzRFMW/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/convert.vcf.gz | /<>/bcftools convert -g -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/R1uRGzRFMW/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/convert.vcf.gz | /<>/bcftools convert -g .,- 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/R1uRGzRFMW/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/R1uRGzRFMW/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/R1uRGzRFMW/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/R1uRGzRFMW/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/R1uRGzRFMW/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/check.vcf.gz | /<>/bcftools convert -g -,. --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/R1uRGzRFMW/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/check.vcf.gz | /<>/bcftools convert -g .,- --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/R1uRGzRFMW/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/R1uRGzRFMW/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/R1uRGzRFMW/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/convert.vcf.gz | /<>/bcftools convert -h -,.,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/R1uRGzRFMW/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/convert.vcf.gz | /<>/bcftools convert -h .,-,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/R1uRGzRFMW/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/convert.vcf.gz | /<>/bcftools convert --hapsample -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/R1uRGzRFMW/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/convert.vcf.gz | /<>/bcftools convert --hapsample .,- 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert --haplegendsample -,.,. /tmp/R1uRGzRFMW/convert.hap-missing.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/R1uRGzRFMW/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/R1uRGzRFMW/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/R1uRGzRFMW/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R1uRGzRFMW/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/R1uRGzRFMW/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/R1uRGzRFMW/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/R1uRGzRFMW/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R1uRGzRFMW/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/R1uRGzRFMW/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab -c /tmp/R1uRGzRFMW/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/R1uRGzRFMW/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R1uRGzRFMW/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/R1uRGzRFMW/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/R1uRGzRFMW/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/R1uRGzRFMW/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R1uRGzRFMW/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R1uRGzRFMW/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R1uRGzRFMW/empty.vcf.gz -f /<>/test/consensus.fa 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/R1uRGzRFMW/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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-donor4.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... [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... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String 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-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/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/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-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-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-donor5.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-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/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/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/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/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/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/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/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/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/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/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/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... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String 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/ENST00000294661/ENST00000294661.fa -g /<>/test/csq/ENST00000294661/ENST00000294661.gff /<>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000294661/ENST00000294661.fa -g /<>/test/csq/ENST00000294661/ENST00000294661.gff /<>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /<>/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/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... [E::vcf_format] Invalid BCF, the INFO index is too large 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/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/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/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/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/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/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/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/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... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String 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/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... [W::vcf_parse] INFO 'PASS' is not defined in the header, assuming Type=String The outputs differ: /<>/test/csq/ENST00000410009/frameshift.txt /<>/test/csq/ENST00000410009/frameshift.txt.new .. failed ... 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... The outputs differ: /<>/test/csq/ENST00000624631/ambiguous.txt /<>/test/csq/ENST00000624631/ambiguous.txt.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/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 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 255 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20190914-1722 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 32440 Build-Time: 36 Distribution: eoan Fail-Stage: build Host Architecture: s390x Install-Time: 6 Job: bcftools_1.9-1.dsc Machine Architecture: s390x Package: bcftools Package-Time: 43 Source-Version: 1.9-1 Space: 32440 Status: attempted Version: 1.9-1 -------------------------------------------------------------------------------- Finished at 20190914-1722 Build needed 00:00:43, 32440k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=eoan --arch=s390x PACKAGEBUILD-17534378 Scanning for processes to kill in build PACKAGEBUILD-17534378