Warning: Permanently added '18.234.111.209' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/10066101-epel-10-aarch64 --chroot epel-10-aarch64 Version: 1.6 PID: 9267 Logging PID: 9269 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 10066101, 'buildroot_pkgs': [], 'chroot': 'epel-10-aarch64', 'enable_net': False, 'fedora_review': False, 'git_hash': '7afd4b414b02c829eb5656fa17d98633a259ea94', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/samtools', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'samtools', 'package_version': '1.23-1', 'project_dirname': 'bioinformatics', 'project_name': 'bioinformatics', 'project_owner': 'ron', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ron/bioinformatics/epel-10-aarch64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'ron/bioinformatics--ron', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'ron', 'tags': [], 'task_id': '10066101-epel-10-aarch64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/samtools /var/lib/copr-rpmbuild/workspace/workdir-ffq5jrsp/samtools --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/samtools', '/var/lib/copr-rpmbuild/workspace/workdir-ffq5jrsp/samtools', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-ffq5jrsp/samtools'... Running: git checkout 7afd4b414b02c829eb5656fa17d98633a259ea94 -- cmd: ['git', 'checkout', '7afd4b414b02c829eb5656fa17d98633a259ea94', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-ffq5jrsp/samtools rc: 0 stdout: stderr: Note: switching to '7afd4b414b02c829eb5656fa17d98633a259ea94'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 7afd4b4 automatic import of samtools Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-ffq5jrsp/samtools rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading samtools-1.23.tar.bz2 INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o samtools-1.23.tar.bz2 --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/ron/bioinformatics/samtools/samtools-1.23.tar.bz2/md5/7ce93103e5a3796c0009f879853837bb/samtools-1.23.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 9138k 100 9138k 0 0 90.6M 0 --:--:-- --:--:-- --:--:-- 90.1M INFO: Reading stdout from command: md5sum samtools-1.23.tar.bz2 tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-ffq5jrsp/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-ffq5jrsp/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769501805.999475 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.6 starting (python version = 3.14.2, NVR = mock-6.6-1.fc43), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-ffq5jrsp/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-ffq5jrsp/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769501805.999475 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-ffq5jrsp/samtools/samtools.spec) Config(centos-stream+epel-10-aarch64) Start: clean chroot Finish: clean chroot Mock Version: 6.6 INFO: Mock Version: 6.6 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-bootstrap-1769501805.999475/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using container image: quay.io/centos/centos:stream10 INFO: Pulling image: quay.io/centos/centos:stream10 INFO: Tagging container image as mock-bootstrap-2a976e19-1d1b-4c81-8fc9-05af2c009813 INFO: Checking that c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 image matches host's architecture INFO: Copy content of container c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 to /var/lib/mock/centos-stream+epel-10-aarch64-bootstrap-1769501805.999475/root INFO: mounting c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 with podman image mount INFO: image c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 as /var/lib/containers/storage/overlay/1dc01b598e3ff5390652e58589fa7a58a2d5659c6ca2b463aceb2ed08c570660/merged INFO: umounting image c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 (/var/lib/containers/storage/overlay/1dc01b598e3ff5390652e58589fa7a58a2d5659c6ca2b463aceb2ed08c570660/merged) with podman image umount INFO: Removing image mock-bootstrap-2a976e19-1d1b-4c81-8fc9-05af2c009813 INFO: Package manager dnf4 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-1769501805.999475/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf4 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.1.1-21.el10.aarch64 rpm-sequoia-1.9.0.3-1.el10.aarch64 python3-dnf-4.20.0-19.el10.noarch python3-dnf-plugins-core-4.7.0-10.el10.noarch yum-4.20.0-19.el10.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 15 kB/s | 2.4 kB 00:00 CentOS Stream 10 - BaseOS 27 MB/s | 9.3 MB 00:00 CentOS Stream 10 - AppStream 16 MB/s | 3.5 MB 00:00 CentOS Stream 10 - CRB 9.6 MB/s | 778 kB 00:00 CentOS Stream 10 - Extras packages 84 kB/s | 8.3 kB 00:00 Extra Packages for Enterprise Linux 10 - aarch6 31 MB/s | 6.1 MB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: bash aarch64 5.2.26-6.el10 baseos 1.8 M bzip2 aarch64 1.0.8-25.el10 baseos 54 k centos-stream-release noarch 10.0-19.el10 baseos 30 k coreutils aarch64 9.5-6.el10 baseos 1.1 M cpio aarch64 2.15-3.el10 baseos 290 k diffutils aarch64 3.10-8.el10 baseos 405 k epel-rpm-macros noarch 10-6.el10_2 epel 8.2 k findutils aarch64 1:4.10.0-5.el10 baseos 555 k gawk aarch64 5.3.0-6.el10 baseos 1.1 M glibc-minimal-langpack aarch64 2.39-99.el10 baseos 39 k grep aarch64 3.11-10.el10 baseos 298 k gzip aarch64 1.13-3.el10 baseos 168 k info aarch64 7.1-6.el10 baseos 182 k patch aarch64 2.7.6-26.el10 appstream 130 k redhat-rpm-config noarch 295-1.el10 appstream 74 k rpm-build aarch64 4.19.1.1-21.el10 appstream 76 k sed aarch64 4.9-3.el10 baseos 316 k shadow-utils aarch64 2:4.15.0-9.el10 baseos 1.3 M tar aarch64 2:1.35-10.el10 baseos 857 k unzip aarch64 6.0-69.el10 baseos 186 k util-linux aarch64 2.40.2-13.el10 baseos 1.2 M which aarch64 2.21-44.el10 baseos 42 k xz aarch64 1:5.6.2-4.el10 baseos 481 k Installing dependencies: alternatives aarch64 1.30-2.el10 baseos 41 k ansible-srpm-macros noarch 1-16.1.el10_0 epel 20 k audit-libs aarch64 4.0.3-5.el10 baseos 129 k authselect aarch64 1.5.0-8.el10 baseos 144 k authselect-libs aarch64 1.5.0-8.el10 baseos 221 k basesystem noarch 11-22.el10 baseos 4.3 k binutils aarch64 2.41-60.el10 baseos 6.7 M binutils-gold aarch64 2.41-60.el10 baseos 938 k bzip2-libs aarch64 1.0.8-25.el10 baseos 42 k ca-certificates noarch 2025.2.80_v9.0.305-102.el10 baseos 1.1 M centos-gpg-keys noarch 10.0-19.el10 baseos 26 k centos-stream-repos noarch 10.0-19.el10 baseos 12 k coreutils-common aarch64 9.5-6.el10 baseos 2.1 M cracklib aarch64 2.9.11-8.el10 baseos 96 k cracklib-dicts aarch64 2.9.11-8.el10 baseos 3.6 M crypto-policies noarch 20251127-1.git27c2902.el10 baseos 98 k curl aarch64 8.12.1-4.el10 baseos 214 k cyrus-sasl-lib aarch64 2.1.28-27.el10 baseos 107 k debugedit aarch64 5.1-8.el10 appstream 80 k dwz aarch64 0.16-1.el10 appstream 137 k ed aarch64 1.20-5.el10 baseos 82 k efi-srpm-macros noarch 6-6.el10 appstream 24 k elfutils aarch64 0.194-1.el10 baseos 539 k elfutils-debuginfod-client aarch64 0.194-1.el10 baseos 42 k elfutils-default-yama-scope noarch 0.194-1.el10 baseos 8.3 k elfutils-libelf aarch64 0.194-1.el10 baseos 199 k elfutils-libs aarch64 0.194-1.el10 baseos 263 k file aarch64 5.45-8.el10 baseos 49 k file-libs aarch64 5.45-8.el10 baseos 762 k filesystem aarch64 3.18-17.el10 baseos 4.8 M fonts-srpm-macros noarch 1:2.0.5-18.el10 appstream 27 k forge-srpm-macros noarch 0.4.0-6.el10 appstream 21 k fpc-srpm-macros noarch 1.3-7.el10_1 epel 7.8 k gdb-minimal aarch64 16.3-2.el10 appstream 4.1 M gdbm aarch64 1:1.23-14.el10 baseos 150 k gdbm-libs aarch64 1:1.23-14.el10 baseos 56 k ghc-srpm-macros noarch 1.9.2-1.el10_0 epel 9.1 k glibc aarch64 2.39-99.el10 baseos 1.7 M glibc-common aarch64 2.39-99.el10 baseos 321 k glibc-gconv-extra aarch64 2.39-99.el10 baseos 1.8 M gmp aarch64 1:6.2.1-12.el10 baseos 268 k go-srpm-macros noarch 3.8.0-1.el10 appstream 27 k jansson aarch64 2.14-3.el10 baseos 47 k json-c aarch64 0.18-3.el10 baseos 46 k kernel-srpm-macros noarch 1.0-27.el10 appstream 8.7 k keyutils-libs aarch64 1.6.3-5.el10 baseos 33 k krb5-libs aarch64 1.21.3-8.el10 baseos 769 k libacl aarch64 2.3.2-4.el10 baseos 26 k libarchive aarch64 3.7.7-4.el10 baseos 406 k libattr aarch64 2.5.2-5.el10 baseos 19 k libblkid aarch64 2.40.2-13.el10 baseos 123 k libbrotli aarch64 1.1.0-7.el10 baseos 344 k libcap aarch64 2.69-7.el10 baseos 91 k libcap-ng aarch64 0.8.4-6.el10 baseos 33 k libcom_err aarch64 1.47.1-5.el10 baseos 26 k libcurl aarch64 8.12.1-4.el10 baseos 361 k libeconf aarch64 0.6.2-4.el10 baseos 33 k libevent aarch64 2.1.12-16.el10 baseos 256 k libfdisk aarch64 2.40.2-13.el10 baseos 154 k libffi aarch64 3.4.4-10.el10 baseos 38 k libgcc aarch64 14.3.1-4.2.el10 baseos 130 k libgomp aarch64 14.3.1-4.2.el10 baseos 361 k libidn2 aarch64 2.3.7-3.el10 baseos 119 k libmount aarch64 2.40.2-13.el10 baseos 153 k libnghttp2 aarch64 1.64.0-2.el10 baseos 77 k libpkgconf aarch64 2.1.0-3.el10 baseos 39 k libpsl aarch64 0.21.5-6.el10 baseos 65 k libpwquality aarch64 1.4.5-12.el10 baseos 123 k libselinux aarch64 3.9-3.el10 baseos 96 k libsemanage aarch64 3.9-2.el10 baseos 118 k libsepol aarch64 3.9-1.el10 baseos 331 k libsmartcols aarch64 2.40.2-13.el10 baseos 82 k libssh aarch64 0.11.1-3.el10 baseos 231 k libssh-config noarch 0.11.1-3.el10 baseos 8.4 k libstdc++ aarch64 14.3.1-4.2.el10 baseos 871 k libtasn1 aarch64 4.20.0-1.el10 baseos 74 k libunistring aarch64 1.1-10.el10 baseos 540 k libutempter aarch64 1.2.1-15.el10 baseos 28 k libuuid aarch64 2.40.2-13.el10 baseos 28 k libverto aarch64 0.3.2-10.el10 baseos 22 k libxcrypt aarch64 4.4.36-10.el10 baseos 124 k libxml2 aarch64 2.12.5-9.el10 baseos 673 k libzstd aarch64 1.5.5-9.el10 baseos 285 k lua-libs aarch64 5.4.6-7.el10 baseos 130 k lua-srpm-macros noarch 1-15.el10 appstream 9.8 k lz4-libs aarch64 1.9.4-8.el10 baseos 68 k mpfr aarch64 4.2.1-6.el10 baseos 324 k ncurses-base noarch 6.4-14.20240127.el10 baseos 100 k ncurses-libs aarch64 6.4-14.20240127.el10 baseos 330 k ocaml-srpm-macros noarch 10-4.el10 appstream 10 k openblas-srpm-macros noarch 2-19.el10 appstream 8.7 k openldap aarch64 2.6.10-1.el10 baseos 235 k openssl-fips-provider aarch64 1:3.5.1-6.el10 baseos 716 k openssl-libs aarch64 1:3.5.1-6.el10 baseos 2.1 M p11-kit aarch64 0.26.1-1.el10 baseos 535 k p11-kit-trust aarch64 0.26.1-1.el10 baseos 141 k package-notes-srpm-macros noarch 0.5-13.el10 appstream 10 k pam aarch64 1.6.1-9.el10 baseos 589 k pam-libs aarch64 1.6.1-9.el10 baseos 56 k pcre2 aarch64 10.44-1.el10.3 baseos 227 k pcre2-syntax noarch 10.44-1.el10.3 baseos 151 k perl-srpm-macros noarch 1-57.el10 appstream 9.5 k pkgconf aarch64 2.1.0-3.el10 baseos 44 k pkgconf-m4 noarch 2.1.0-3.el10 baseos 15 k pkgconf-pkg-config aarch64 2.1.0-3.el10 baseos 11 k popt aarch64 1.19-8.el10 baseos 65 k publicsuffix-list-dafsa noarch 20240107-5.el10 baseos 59 k pyproject-srpm-macros noarch 1.18.5-1.el10 appstream 13 k python-srpm-macros noarch 3.12-11.el10 appstream 22 k qt6-srpm-macros noarch 6.10.1-1.el10 appstream 9.1 k readline aarch64 8.2-11.el10 baseos 212 k rpm aarch64 4.19.1.1-21.el10 baseos 562 k rpm-build-libs aarch64 4.19.1.1-21.el10 baseos 88 k rpm-libs aarch64 4.19.1.1-21.el10 baseos 298 k rpm-sequoia aarch64 1.9.0.3-1.el10 baseos 902 k rust-toolset-srpm-macros noarch 1.92.0-1.el10 appstream 11 k setup noarch 2.14.5-7.el10 baseos 153 k sqlite-libs aarch64 3.46.1-5.el10 baseos 730 k systemd-libs aarch64 257-21.el10 baseos 788 k util-linux-core aarch64 2.40.2-13.el10 baseos 543 k xz-libs aarch64 1:5.6.2-4.el10 baseos 110 k zip aarch64 3.0-45.el10 baseos 264 k zlib-ng-compat aarch64 2.2.3-3.el10 baseos 63 k zstd aarch64 1.5.5-9.el10 baseos 455 k Transaction Summary ================================================================================ Install 147 Packages Total download size: 60 M Installed size: 215 M Downloading Packages: (1/147): alternatives-1.30-2.el10.aarch64.rpm 3.1 MB/s | 41 kB 00:00 (2/147): authselect-1.5.0-8.el10.aarch64.rpm 7.7 MB/s | 144 kB 00:00 (3/147): authselect-libs-1.5.0-8.el10.aarch64.r 38 MB/s | 221 kB 00:00 (4/147): audit-libs-4.0.3-5.el10.aarch64.rpm 6.3 MB/s | 129 kB 00:00 (5/147): basesystem-11-22.el10.noarch.rpm 2.2 MB/s | 4.3 kB 00:00 (6/147): bash-5.2.26-6.el10.aarch64.rpm 120 MB/s | 1.8 MB 00:00 (7/147): binutils-gold-2.41-60.el10.aarch64.rpm 49 MB/s | 938 kB 00:00 (8/147): binutils-2.41-60.el10.aarch64.rpm 158 MB/s | 6.7 MB 00:00 (9/147): bzip2-1.0.8-25.el10.aarch64.rpm 1.8 MB/s | 54 kB 00:00 (10/147): bzip2-libs-1.0.8-25.el10.aarch64.rpm 1.7 MB/s | 42 kB 00:00 (11/147): centos-gpg-keys-10.0-19.el10.noarch.r 8.3 MB/s | 26 kB 00:00 (12/147): centos-stream-release-10.0-19.el10.no 8.3 MB/s | 30 kB 00:00 (13/147): ca-certificates-2025.2.80_v9.0.305-10 119 MB/s | 1.1 MB 00:00 (14/147): centos-stream-repos-10.0-19.el10.noar 2.1 MB/s | 12 kB 00:00 (15/147): coreutils-9.5-6.el10.aarch64.rpm 112 MB/s | 1.1 MB 00:00 (16/147): coreutils-common-9.5-6.el10.aarch64.r 153 MB/s | 2.1 MB 00:00 (17/147): cpio-2.15-3.el10.aarch64.rpm 19 MB/s | 290 kB 00:00 (18/147): cracklib-2.9.11-8.el10.aarch64.rpm 8.4 MB/s | 96 kB 00:00 (19/147): crypto-policies-20251127-1.git27c2902 8.2 MB/s | 98 kB 00:00 (20/147): cracklib-dicts-2.9.11-8.el10.aarch64. 185 MB/s | 3.6 MB 00:00 (21/147): curl-8.12.1-4.el10.aarch64.rpm 11 MB/s | 214 kB 00:00 (22/147): cyrus-sasl-lib-2.1.28-27.el10.aarch64 12 MB/s | 107 kB 00:00 (23/147): diffutils-3.10-8.el10.aarch64.rpm 83 MB/s | 405 kB 00:00 (24/147): ed-1.20-5.el10.aarch64.rpm 18 MB/s | 82 kB 00:00 (25/147): elfutils-0.194-1.el10.aarch64.rpm 90 MB/s | 539 kB 00:00 (26/147): elfutils-debuginfod-client-0.194-1.el 13 MB/s | 42 kB 00:00 (27/147): elfutils-default-yama-scope-0.194-1.e 3.2 MB/s | 8.3 kB 00:00 (28/147): file-5.45-8.el10.aarch64.rpm 21 MB/s | 49 kB 00:00 (29/147): elfutils-libelf-0.194-1.el10.aarch64. 43 MB/s | 199 kB 00:00 (30/147): elfutils-libs-0.194-1.el10.aarch64.rp 51 MB/s | 263 kB 00:00 (31/147): file-libs-5.45-8.el10.aarch64.rpm 101 MB/s | 762 kB 00:00 (32/147): filesystem-3.18-17.el10.aarch64.rpm 188 MB/s | 4.8 MB 00:00 (33/147): findutils-4.10.0-5.el10.aarch64.rpm 20 MB/s | 555 kB 00:00 (34/147): gawk-5.3.0-6.el10.aarch64.rpm 41 MB/s | 1.1 MB 00:00 (35/147): gdbm-libs-1.23-14.el10.aarch64.rpm 12 MB/s | 56 kB 00:00 (36/147): gdbm-1.23-14.el10.aarch64.rpm 19 MB/s | 150 kB 00:00 (37/147): glibc-2.39-99.el10.aarch64.rpm 160 MB/s | 1.7 MB 00:00 (38/147): glibc-common-2.39-99.el10.aarch64.rpm 26 MB/s | 321 kB 00:00 (39/147): glibc-gconv-extra-2.39-99.el10.aarch6 98 MB/s | 1.8 MB 00:00 (40/147): glibc-minimal-langpack-2.39-99.el10.a 4.5 MB/s | 39 kB 00:00 (41/147): gmp-6.2.1-12.el10.aarch64.rpm 31 MB/s | 268 kB 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(144/147): epel-rpm-macros-10-6.el10_2.noarch.r 926 kB/s | 8.2 kB 00:00 (145/147): fpc-srpm-macros-1.3-7.el10_1.noarch. 820 kB/s | 7.8 kB 00:00 (146/147): ghc-srpm-macros-1.9.2-1.el10_0.noarc 4.3 MB/s | 9.1 kB 00:00 (147/147): ansible-srpm-macros-1-16.1.el10_0.no 1.6 MB/s | 20 kB 00:00 -------------------------------------------------------------------------------- Total 101 MB/s | 60 MB 00:00 CentOS Stream 10 - BaseOS 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x8483C65D: Userid : "CentOS (CentOS Official Signing Key) " Fingerprint: 99DB 70FA E1D7 CE22 7FB6 4882 05B5 55B3 8483 C65D From : /usr/share/distribution-gpg-keys/centos/RPM-GPG-KEY-CentOS-Official-SHA256 Key imported successfully Extra Packages for Enterprise Linux 10 - aarch6 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xE37ED158: Userid : "Fedora (epel10) " Fingerprint: 7D8D 15CB FC4E 6268 8591 FB26 33D9 8517 E37E D158 From : /usr/share/distribution-gpg-keys/epel/RPM-GPG-KEY-EPEL-10 Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-17.el10.aarch64 1/1 Preparing : 1/1 Installing : libgcc-14.3.1-4.2.el10.aarch64 1/147 Running scriptlet: libgcc-14.3.1-4.2.el10.aarch64 1/147 Installing : ghc-srpm-macros-1.9.2-1.el10_0.noarch 2/147 Installing : fpc-srpm-macros-1.3-7.el10_1.noarch 3/147 Installing : ansible-srpm-macros-1-16.1.el10_0.noarch 4/147 Installing : rust-toolset-srpm-macros-1.92.0-1.el10.noarch 5/147 Installing : qt6-srpm-macros-6.10.1-1.el10.noarch 6/147 Installing : perl-srpm-macros-1-57.el10.noarch 7/147 Installing : package-notes-srpm-macros-0.5-13.el10.noarch 8/147 Installing : openblas-srpm-macros-2-19.el10.noarch 9/147 Installing : ocaml-srpm-macros-10-4.el10.noarch 10/147 Installing : kernel-srpm-macros-1.0-27.el10.noarch 11/147 Installing : publicsuffix-list-dafsa-20240107-5.el10.noarch 12/147 Installing : pkgconf-m4-2.1.0-3.el10.noarch 13/147 Installing : pcre2-syntax-10.44-1.el10.3.noarch 14/147 Installing : 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81/147 Installing : p11-kit-0.26.1-1.el10.aarch64 82/147 Installing : p11-kit-trust-0.26.1-1.el10.aarch64 83/147 Running scriptlet: p11-kit-trust-0.26.1-1.el10.aarch64 83/147 Installing : openssl-fips-provider-1:3.5.1-6.el10.aarch64 84/147 Installing : openssl-libs-1:3.5.1-6.el10.aarch64 85/147 Installing : coreutils-9.5-6.el10.aarch64 86/147 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar 87/147 Installing : ca-certificates-2025.2.80_v9.0.305-102.el10.noar 87/147 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar 87/147 Installing : authselect-libs-1.5.0-8.el10.aarch64 88/147 Installing : gzip-1.13-3.el10.aarch64 89/147 Installing : cracklib-2.9.11-8.el10.aarch64 90/147 Installing : cracklib-dicts-2.9.11-8.el10.aarch64 91/147 Installing : libpwquality-1.4.5-12.el10.aarch64 92/147 Installing : libevent-2.1.12-16.el10.aarch64 93/147 Installing : rpm-sequoia-1.9.0.3-1.el10.aarch64 94/147 Installing : zip-3.0-45.el10.aarch64 95/147 Installing : cyrus-sasl-lib-2.1.28-27.el10.aarch64 96/147 Installing : openldap-2.6.10-1.el10.aarch64 97/147 Installing : gdbm-1:1.23-14.el10.aarch64 98/147 Installing : pam-1.6.1-9.el10.aarch64 99/147 Installing : libfdisk-2.40.2-13.el10.aarch64 100/147 Installing : libxml2-2.12.5-9.el10.aarch64 101/147 Installing : libarchive-3.7.7-4.el10.aarch64 102/147 Installing : bzip2-1.0.8-25.el10.aarch64 103/147 Installing : sqlite-libs-3.46.1-5.el10.aarch64 104/147 Installing : rpm-libs-4.19.1.1-21.el10.aarch64 105/147 Installing : ed-1.20-5.el10.aarch64 106/147 Installing : patch-2.7.6-26.el10.aarch64 107/147 Installing : elfutils-default-yama-scope-0.194-1.el10.noarch 108/147 Running scriptlet: elfutils-default-yama-scope-0.194-1.el10.noarch 108/147 Installing : cpio-2.15-3.el10.aarch64 109/147 Installing : diffutils-3.10-8.el10.aarch64 110/147 Installing : json-c-0.18-3.el10.aarch64 111/147 Installing : keyutils-libs-1.6.3-5.el10.aarch64 112/147 Installing : libbrotli-1.1.0-7.el10.aarch64 113/147 Installing : libcom_err-1.47.1-5.el10.aarch64 114/147 Installing : libgomp-14.3.1-4.2.el10.aarch64 115/147 Installing : libnghttp2-1.64.0-2.el10.aarch64 116/147 Installing : libpkgconf-2.1.0-3.el10.aarch64 117/147 Installing : pkgconf-2.1.0-3.el10.aarch64 118/147 Installing : pkgconf-pkg-config-2.1.0-3.el10.aarch64 119/147 Installing : libverto-0.3.2-10.el10.aarch64 120/147 Installing : krb5-libs-1.21.3-8.el10.aarch64 121/147 Installing : libssh-0.11.1-3.el10.aarch64 122/147 Installing : libcurl-8.12.1-4.el10.aarch64 123/147 Installing : elfutils-libs-0.194-1.el10.aarch64 124/147 Installing : elfutils-debuginfod-client-0.194-1.el10.aarch64 125/147 Installing : binutils-gold-2.41-60.el10.aarch64 126/147 Running scriptlet: binutils-gold-2.41-60.el10.aarch64 126/147 Installing : binutils-2.41-60.el10.aarch64 127/147 Running scriptlet: binutils-2.41-60.el10.aarch64 127/147 Installing : elfutils-0.194-1.el10.aarch64 128/147 Installing : gdb-minimal-16.3-2.el10.aarch64 129/147 Installing : debugedit-5.1-8.el10.aarch64 130/147 Installing : rpm-build-libs-4.19.1.1-21.el10.aarch64 131/147 Installing : curl-8.12.1-4.el10.aarch64 132/147 Running scriptlet: rpm-4.19.1.1-21.el10.aarch64 133/147 Installing : rpm-4.19.1.1-21.el10.aarch64 133/147 Installing : efi-srpm-macros-6-6.el10.noarch 134/147 Installing : lua-srpm-macros-1-15.el10.noarch 135/147 Installing : fonts-srpm-macros-1:2.0.5-18.el10.noarch 136/147 Installing : forge-srpm-macros-0.4.0-6.el10.noarch 137/147 Installing : go-srpm-macros-3.8.0-1.el10.noarch 138/147 Installing : python-srpm-macros-3.12-11.el10.noarch 139/147 Installing : redhat-rpm-config-295-1.el10.noarch 140/147 Installing : rpm-build-4.19.1.1-21.el10.aarch64 141/147 Installing : pyproject-srpm-macros-1.18.5-1.el10.noarch 142/147 Installing : util-linux-2.40.2-13.el10.aarch64 143/147 Running scriptlet: util-linux-2.40.2-13.el10.aarch64 143/147 Installing : authselect-1.5.0-8.el10.aarch64 144/147 Installing : which-2.21-44.el10.aarch64 145/147 Installing : info-7.1-6.el10.aarch64 146/147 Installing : epel-rpm-macros-10-6.el10_2.noarch 147/147 Running scriptlet: filesystem-3.18-17.el10.aarch64 147/147 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar 147/147 Running scriptlet: authselect-libs-1.5.0-8.el10.aarch64 147/147 Running scriptlet: rpm-4.19.1.1-21.el10.aarch64 147/147 Running scriptlet: epel-rpm-macros-10-6.el10_2.noarch 147/147 Installed: alternatives-1.30-2.el10.aarch64 ansible-srpm-macros-1-16.1.el10_0.noarch audit-libs-4.0.3-5.el10.aarch64 authselect-1.5.0-8.el10.aarch64 authselect-libs-1.5.0-8.el10.aarch64 basesystem-11-22.el10.noarch bash-5.2.26-6.el10.aarch64 binutils-2.41-60.el10.aarch64 binutils-gold-2.41-60.el10.aarch64 bzip2-1.0.8-25.el10.aarch64 bzip2-libs-1.0.8-25.el10.aarch64 ca-certificates-2025.2.80_v9.0.305-102.el10.noarch centos-gpg-keys-10.0-19.el10.noarch centos-stream-release-10.0-19.el10.noarch centos-stream-repos-10.0-19.el10.noarch coreutils-9.5-6.el10.aarch64 coreutils-common-9.5-6.el10.aarch64 cpio-2.15-3.el10.aarch64 cracklib-2.9.11-8.el10.aarch64 cracklib-dicts-2.9.11-8.el10.aarch64 crypto-policies-20251127-1.git27c2902.el10.noarch curl-8.12.1-4.el10.aarch64 cyrus-sasl-lib-2.1.28-27.el10.aarch64 debugedit-5.1-8.el10.aarch64 diffutils-3.10-8.el10.aarch64 dwz-0.16-1.el10.aarch64 ed-1.20-5.el10.aarch64 efi-srpm-macros-6-6.el10.noarch elfutils-0.194-1.el10.aarch64 elfutils-debuginfod-client-0.194-1.el10.aarch64 elfutils-default-yama-scope-0.194-1.el10.noarch elfutils-libelf-0.194-1.el10.aarch64 elfutils-libs-0.194-1.el10.aarch64 epel-rpm-macros-10-6.el10_2.noarch file-5.45-8.el10.aarch64 file-libs-5.45-8.el10.aarch64 filesystem-3.18-17.el10.aarch64 findutils-1:4.10.0-5.el10.aarch64 fonts-srpm-macros-1:2.0.5-18.el10.noarch forge-srpm-macros-0.4.0-6.el10.noarch fpc-srpm-macros-1.3-7.el10_1.noarch gawk-5.3.0-6.el10.aarch64 gdb-minimal-16.3-2.el10.aarch64 gdbm-1:1.23-14.el10.aarch64 gdbm-libs-1:1.23-14.el10.aarch64 ghc-srpm-macros-1.9.2-1.el10_0.noarch glibc-2.39-99.el10.aarch64 glibc-common-2.39-99.el10.aarch64 glibc-gconv-extra-2.39-99.el10.aarch64 glibc-minimal-langpack-2.39-99.el10.aarch64 gmp-1:6.2.1-12.el10.aarch64 go-srpm-macros-3.8.0-1.el10.noarch grep-3.11-10.el10.aarch64 gzip-1.13-3.el10.aarch64 info-7.1-6.el10.aarch64 jansson-2.14-3.el10.aarch64 json-c-0.18-3.el10.aarch64 kernel-srpm-macros-1.0-27.el10.noarch keyutils-libs-1.6.3-5.el10.aarch64 krb5-libs-1.21.3-8.el10.aarch64 libacl-2.3.2-4.el10.aarch64 libarchive-3.7.7-4.el10.aarch64 libattr-2.5.2-5.el10.aarch64 libblkid-2.40.2-13.el10.aarch64 libbrotli-1.1.0-7.el10.aarch64 libcap-2.69-7.el10.aarch64 libcap-ng-0.8.4-6.el10.aarch64 libcom_err-1.47.1-5.el10.aarch64 libcurl-8.12.1-4.el10.aarch64 libeconf-0.6.2-4.el10.aarch64 libevent-2.1.12-16.el10.aarch64 libfdisk-2.40.2-13.el10.aarch64 libffi-3.4.4-10.el10.aarch64 libgcc-14.3.1-4.2.el10.aarch64 libgomp-14.3.1-4.2.el10.aarch64 libidn2-2.3.7-3.el10.aarch64 libmount-2.40.2-13.el10.aarch64 libnghttp2-1.64.0-2.el10.aarch64 libpkgconf-2.1.0-3.el10.aarch64 libpsl-0.21.5-6.el10.aarch64 libpwquality-1.4.5-12.el10.aarch64 libselinux-3.9-3.el10.aarch64 libsemanage-3.9-2.el10.aarch64 libsepol-3.9-1.el10.aarch64 libsmartcols-2.40.2-13.el10.aarch64 libssh-0.11.1-3.el10.aarch64 libssh-config-0.11.1-3.el10.noarch libstdc++-14.3.1-4.2.el10.aarch64 libtasn1-4.20.0-1.el10.aarch64 libunistring-1.1-10.el10.aarch64 libutempter-1.2.1-15.el10.aarch64 libuuid-2.40.2-13.el10.aarch64 libverto-0.3.2-10.el10.aarch64 libxcrypt-4.4.36-10.el10.aarch64 libxml2-2.12.5-9.el10.aarch64 libzstd-1.5.5-9.el10.aarch64 lua-libs-5.4.6-7.el10.aarch64 lua-srpm-macros-1-15.el10.noarch lz4-libs-1.9.4-8.el10.aarch64 mpfr-4.2.1-6.el10.aarch64 ncurses-base-6.4-14.20240127.el10.noarch ncurses-libs-6.4-14.20240127.el10.aarch64 ocaml-srpm-macros-10-4.el10.noarch openblas-srpm-macros-2-19.el10.noarch openldap-2.6.10-1.el10.aarch64 openssl-fips-provider-1:3.5.1-6.el10.aarch64 openssl-libs-1:3.5.1-6.el10.aarch64 p11-kit-0.26.1-1.el10.aarch64 p11-kit-trust-0.26.1-1.el10.aarch64 package-notes-srpm-macros-0.5-13.el10.noarch pam-1.6.1-9.el10.aarch64 pam-libs-1.6.1-9.el10.aarch64 patch-2.7.6-26.el10.aarch64 pcre2-10.44-1.el10.3.aarch64 pcre2-syntax-10.44-1.el10.3.noarch perl-srpm-macros-1-57.el10.noarch pkgconf-2.1.0-3.el10.aarch64 pkgconf-m4-2.1.0-3.el10.noarch pkgconf-pkg-config-2.1.0-3.el10.aarch64 popt-1.19-8.el10.aarch64 publicsuffix-list-dafsa-20240107-5.el10.noarch pyproject-srpm-macros-1.18.5-1.el10.noarch python-srpm-macros-3.12-11.el10.noarch qt6-srpm-macros-6.10.1-1.el10.noarch readline-8.2-11.el10.aarch64 redhat-rpm-config-295-1.el10.noarch rpm-4.19.1.1-21.el10.aarch64 rpm-build-4.19.1.1-21.el10.aarch64 rpm-build-libs-4.19.1.1-21.el10.aarch64 rpm-libs-4.19.1.1-21.el10.aarch64 rpm-sequoia-1.9.0.3-1.el10.aarch64 rust-toolset-srpm-macros-1.92.0-1.el10.noarch sed-4.9-3.el10.aarch64 setup-2.14.5-7.el10.noarch shadow-utils-2:4.15.0-9.el10.aarch64 sqlite-libs-3.46.1-5.el10.aarch64 systemd-libs-257-21.el10.aarch64 tar-2:1.35-10.el10.aarch64 unzip-6.0-69.el10.aarch64 util-linux-2.40.2-13.el10.aarch64 util-linux-core-2.40.2-13.el10.aarch64 which-2.21-44.el10.aarch64 xz-1:5.6.2-4.el10.aarch64 xz-libs-1:5.6.2-4.el10.aarch64 zip-3.0-45.el10.aarch64 zlib-ng-compat-2.2.3-3.el10.aarch64 zstd-1.5.5-9.el10.aarch64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.30-2.el10.aarch64 ansible-srpm-macros-1-16.1.el10_0.noarch audit-libs-4.0.3-5.el10.aarch64 authselect-1.5.0-8.el10.aarch64 authselect-libs-1.5.0-8.el10.aarch64 basesystem-11-22.el10.noarch bash-5.2.26-6.el10.aarch64 binutils-2.41-60.el10.aarch64 binutils-gold-2.41-60.el10.aarch64 bzip2-1.0.8-25.el10.aarch64 bzip2-libs-1.0.8-25.el10.aarch64 ca-certificates-2025.2.80_v9.0.305-102.el10.noarch centos-gpg-keys-10.0-19.el10.noarch centos-stream-release-10.0-19.el10.noarch centos-stream-repos-10.0-19.el10.noarch coreutils-9.5-6.el10.aarch64 coreutils-common-9.5-6.el10.aarch64 cpio-2.15-3.el10.aarch64 cracklib-2.9.11-8.el10.aarch64 cracklib-dicts-2.9.11-8.el10.aarch64 crypto-policies-20251127-1.git27c2902.el10.noarch curl-8.12.1-4.el10.aarch64 cyrus-sasl-lib-2.1.28-27.el10.aarch64 debugedit-5.1-8.el10.aarch64 diffutils-3.10-8.el10.aarch64 dwz-0.16-1.el10.aarch64 ed-1.20-5.el10.aarch64 efi-srpm-macros-6-6.el10.noarch elfutils-0.194-1.el10.aarch64 elfutils-debuginfod-client-0.194-1.el10.aarch64 elfutils-default-yama-scope-0.194-1.el10.noarch elfutils-libelf-0.194-1.el10.aarch64 elfutils-libs-0.194-1.el10.aarch64 epel-rpm-macros-10-6.el10_2.noarch file-5.45-8.el10.aarch64 file-libs-5.45-8.el10.aarch64 filesystem-3.18-17.el10.aarch64 findutils-4.10.0-5.el10.aarch64 fonts-srpm-macros-2.0.5-18.el10.noarch forge-srpm-macros-0.4.0-6.el10.noarch fpc-srpm-macros-1.3-7.el10_1.noarch gawk-5.3.0-6.el10.aarch64 gdb-minimal-16.3-2.el10.aarch64 gdbm-1.23-14.el10.aarch64 gdbm-libs-1.23-14.el10.aarch64 ghc-srpm-macros-1.9.2-1.el10_0.noarch glibc-2.39-99.el10.aarch64 glibc-common-2.39-99.el10.aarch64 glibc-gconv-extra-2.39-99.el10.aarch64 glibc-minimal-langpack-2.39-99.el10.aarch64 gmp-6.2.1-12.el10.aarch64 go-srpm-macros-3.8.0-1.el10.noarch gpg-pubkey-8483c65d-5ccc5b19 gpg-pubkey-e37ed158-65785fa9 grep-3.11-10.el10.aarch64 gzip-1.13-3.el10.aarch64 info-7.1-6.el10.aarch64 jansson-2.14-3.el10.aarch64 json-c-0.18-3.el10.aarch64 kernel-srpm-macros-1.0-27.el10.noarch keyutils-libs-1.6.3-5.el10.aarch64 krb5-libs-1.21.3-8.el10.aarch64 libacl-2.3.2-4.el10.aarch64 libarchive-3.7.7-4.el10.aarch64 libattr-2.5.2-5.el10.aarch64 libblkid-2.40.2-13.el10.aarch64 libbrotli-1.1.0-7.el10.aarch64 libcap-2.69-7.el10.aarch64 libcap-ng-0.8.4-6.el10.aarch64 libcom_err-1.47.1-5.el10.aarch64 libcurl-8.12.1-4.el10.aarch64 libeconf-0.6.2-4.el10.aarch64 libevent-2.1.12-16.el10.aarch64 libfdisk-2.40.2-13.el10.aarch64 libffi-3.4.4-10.el10.aarch64 libgcc-14.3.1-4.2.el10.aarch64 libgomp-14.3.1-4.2.el10.aarch64 libidn2-2.3.7-3.el10.aarch64 libmount-2.40.2-13.el10.aarch64 libnghttp2-1.64.0-2.el10.aarch64 libpkgconf-2.1.0-3.el10.aarch64 libpsl-0.21.5-6.el10.aarch64 libpwquality-1.4.5-12.el10.aarch64 libselinux-3.9-3.el10.aarch64 libsemanage-3.9-2.el10.aarch64 libsepol-3.9-1.el10.aarch64 libsmartcols-2.40.2-13.el10.aarch64 libssh-0.11.1-3.el10.aarch64 libssh-config-0.11.1-3.el10.noarch libstdc++-14.3.1-4.2.el10.aarch64 libtasn1-4.20.0-1.el10.aarch64 libunistring-1.1-10.el10.aarch64 libutempter-1.2.1-15.el10.aarch64 libuuid-2.40.2-13.el10.aarch64 libverto-0.3.2-10.el10.aarch64 libxcrypt-4.4.36-10.el10.aarch64 libxml2-2.12.5-9.el10.aarch64 libzstd-1.5.5-9.el10.aarch64 lua-libs-5.4.6-7.el10.aarch64 lua-srpm-macros-1-15.el10.noarch lz4-libs-1.9.4-8.el10.aarch64 mpfr-4.2.1-6.el10.aarch64 ncurses-base-6.4-14.20240127.el10.noarch ncurses-libs-6.4-14.20240127.el10.aarch64 ocaml-srpm-macros-10-4.el10.noarch openblas-srpm-macros-2-19.el10.noarch openldap-2.6.10-1.el10.aarch64 openssl-fips-provider-3.5.1-6.el10.aarch64 openssl-libs-3.5.1-6.el10.aarch64 p11-kit-0.26.1-1.el10.aarch64 p11-kit-trust-0.26.1-1.el10.aarch64 package-notes-srpm-macros-0.5-13.el10.noarch pam-1.6.1-9.el10.aarch64 pam-libs-1.6.1-9.el10.aarch64 patch-2.7.6-26.el10.aarch64 pcre2-10.44-1.el10.3.aarch64 pcre2-syntax-10.44-1.el10.3.noarch perl-srpm-macros-1-57.el10.noarch pkgconf-2.1.0-3.el10.aarch64 pkgconf-m4-2.1.0-3.el10.noarch pkgconf-pkg-config-2.1.0-3.el10.aarch64 popt-1.19-8.el10.aarch64 publicsuffix-list-dafsa-20240107-5.el10.noarch pyproject-srpm-macros-1.18.5-1.el10.noarch python-srpm-macros-3.12-11.el10.noarch qt6-srpm-macros-6.10.1-1.el10.noarch readline-8.2-11.el10.aarch64 redhat-rpm-config-295-1.el10.noarch rpm-4.19.1.1-21.el10.aarch64 rpm-build-4.19.1.1-21.el10.aarch64 rpm-build-libs-4.19.1.1-21.el10.aarch64 rpm-libs-4.19.1.1-21.el10.aarch64 rpm-sequoia-1.9.0.3-1.el10.aarch64 rust-toolset-srpm-macros-1.92.0-1.el10.noarch sed-4.9-3.el10.aarch64 setup-2.14.5-7.el10.noarch shadow-utils-4.15.0-9.el10.aarch64 sqlite-libs-3.46.1-5.el10.aarch64 systemd-libs-257-21.el10.aarch64 tar-1.35-10.el10.aarch64 unzip-6.0-69.el10.aarch64 util-linux-2.40.2-13.el10.aarch64 util-linux-core-2.40.2-13.el10.aarch64 which-2.21-44.el10.aarch64 xz-5.6.2-4.el10.aarch64 xz-libs-5.6.2-4.el10.aarch64 zip-3.0-45.el10.aarch64 zlib-ng-compat-2.2.3-3.el10.aarch64 zstd-1.5.5-9.el10.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769040000 Wrote: /builddir/build/SRPMS/samtools-1.23-1.el10.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/centos-stream+epel-10-aarch64-1769501805.999475/root/var/log/dnf.rpm.log /var/lib/mock/centos-stream+epel-10-aarch64-1769501805.999475/root/var/log/dnf.librepo.log /var/lib/mock/centos-stream+epel-10-aarch64-1769501805.999475/root/var/log/dnf.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-ffq5jrsp/samtools/samtools.spec) Config(child) 0 minutes 28 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/samtools-1.23-1.el10.src.rpm) Config(centos-stream+epel-10-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-bootstrap-1769501805.999475/root. INFO: reusing tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-bootstrap-1769501805.999475/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-1769501805.999475/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.1.1-21.el10.aarch64 rpm-sequoia-1.9.0.3-1.el10.aarch64 python3-dnf-4.20.0-19.el10.noarch python3-dnf-plugins-core-4.7.0-10.el10.noarch yum-4.20.0-19.el10.noarch Finish: chroot init Start: build phase for samtools-1.23-1.el10.src.rpm Start: build setup for samtools-1.23-1.el10.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769040000 Wrote: /builddir/build/SRPMS/samtools-1.23-1.el10.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 91 kB/s | 1.5 kB 00:00 CentOS Stream 10 - BaseOS 39 kB/s | 5.5 kB 00:00 CentOS Stream 10 - AppStream 111 kB/s | 5.5 kB 00:00 CentOS Stream 10 - CRB 28 kB/s | 4.4 kB 00:00 CentOS Stream 10 - Extras packages 143 kB/s | 7.4 kB 00:00 Extra Packages for Enterprise Linux 10 - aarch6 363 kB/s | 22 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: gcc aarch64 14.3.1-4.2.el10 appstream 35 M htslib-devel aarch64 1.23-1.el10 copr_base 107 k htslib-tools aarch64 1.23-1.el10 copr_base 740 k make aarch64 1:4.4.1-9.el10 baseos 585 k ncurses-devel aarch64 6.4-14.20240127.el10 appstream 753 k perl-FindBin noarch 1.54-514.el10 appstream 15 k perl-Getopt-Long noarch 1:2.58-3.el10 baseos 65 k perl-interpreter aarch64 4:5.40.2-514.el10 appstream 73 k perl-lib aarch64 0.65-514.el10 appstream 16 k zlib-ng-compat-devel aarch64 2.2.3-3.el10 appstream 36 k Installing dependencies: annobin-docs noarch 13.02-2.el10 appstream 87 k annobin-plugin-gcc aarch64 13.02-2.el10 appstream 997 k cmake-filesystem aarch64 3.31.8-1.el10 appstream 21 k cpp aarch64 14.3.1-4.2.el10 appstream 11 M gcc-plugin-annobin aarch64 14.3.1-4.2.el10 appstream 69 k glibc-devel aarch64 2.39-99.el10 appstream 589 k groff-base aarch64 1.23.0-10.el10 baseos 1.1 M htslib aarch64 1.23-1.el10 copr_base 560 k kernel-headers aarch64 6.12.0-191.el10 appstream 3.1 M libasan aarch64 14.3.1-4.2.el10 appstream 532 k libatomic aarch64 14.3.1-4.2.el10 baseos 58 k libmpc aarch64 1.3.1-7.el10 appstream 73 k libubsan aarch64 14.3.1-4.2.el10 appstream 238 k libxcrypt-devel aarch64 4.4.36-10.el10 appstream 30 k ncurses aarch64 6.4-14.20240127.el10 baseos 421 k ncurses-c++-libs aarch64 6.4-14.20240127.el10 appstream 40 k perl-AutoLoader noarch 5.74-514.el10 appstream 22 k perl-B aarch64 1.89-514.el10 appstream 179 k perl-Carp noarch 1.54-511.el10 baseos 30 k perl-Class-Struct noarch 0.68-514.el10 appstream 23 k perl-Data-Dumper aarch64 2.189-512.el10 baseos 56 k perl-Digest noarch 1.20-511.el10 baseos 26 k perl-Digest-MD5 aarch64 2.59-6.el10 baseos 37 k perl-DynaLoader aarch64 1.56-514.el10 appstream 27 k perl-Encode aarch64 4:3.21-511.el10 baseos 1.1 M perl-Errno aarch64 1.38-514.el10 appstream 16 k perl-Exporter noarch 5.78-511.el10 baseos 32 k perl-Fcntl aarch64 1.18-514.el10 appstream 30 k perl-File-Basename noarch 2.86-514.el10 appstream 18 k perl-File-Path noarch 2.18-512.el10 appstream 35 k perl-File-Temp noarch 1:0.231.100-512.el10 baseos 60 k perl-File-stat noarch 1.14-514.el10 appstream 18 k perl-FileHandle noarch 2.05-514.el10 appstream 16 k perl-Getopt-Std noarch 1.14-514.el10 appstream 16 k perl-HTTP-Tiny noarch 0.088-512.el10 baseos 57 k perl-IO aarch64 1.55-514.el10 appstream 81 k perl-IO-Socket-IP noarch 0.42-512.el10 baseos 43 k perl-IO-Socket-SSL noarch 2.085-3.el10 baseos 227 k perl-IPC-Open3 noarch 1.22-514.el10 appstream 23 k perl-MIME-Base64 aarch64 3.16-511.el10 baseos 31 k perl-Mozilla-CA noarch 20231213-5.el10 baseos 15 k perl-Net-SSLeay aarch64 1.94-8.el10 appstream 381 k perl-POSIX aarch64 2.20-514.el10 appstream 98 k perl-PathTools aarch64 3.91-512.el10 baseos 85 k perl-Pod-Escapes noarch 1:1.07-511.el10 baseos 21 k perl-Pod-Perldoc noarch 3.28.01-512.el10 baseos 84 k perl-Pod-Simple noarch 1:3.45-511.el10 baseos 218 k perl-Pod-Usage noarch 4:2.03-511.el10 baseos 41 k perl-Scalar-List-Utils aarch64 5:1.63-511.el10 baseos 73 k perl-SelectSaver noarch 1.02-514.el10 appstream 12 k perl-Socket aarch64 4:2.038-511.el10 baseos 56 k perl-Storable aarch64 1:3.32-511.el10 baseos 98 k perl-Symbol noarch 1.09-514.el10 appstream 15 k perl-Term-ANSIColor noarch 5.01-512.el10 baseos 49 k perl-Term-Cap noarch 1.18-511.el10 baseos 23 k perl-Text-ParseWords noarch 3.31-511.el10 baseos 17 k perl-Text-Tabs+Wrap noarch 2024.001-511.el10 baseos 23 k perl-Time-Local noarch 2:1.350-511.el10 baseos 35 k perl-URI noarch 5.27-3.el10 baseos 134 k perl-base noarch 2.27-514.el10 appstream 17 k perl-constant noarch 1.33-512.el10 baseos 24 k perl-if noarch 0.61.000-514.el10 appstream 15 k perl-libnet noarch 3.15-512.el10 baseos 127 k perl-libs aarch64 4:5.40.2-514.el10 appstream 2.3 M perl-locale noarch 1.12-514.el10 appstream 14 k perl-mro aarch64 1.29-514.el10 appstream 30 k perl-overload noarch 1.37-514.el10 appstream 46 k perl-overloading noarch 0.02-514.el10 appstream 14 k perl-parent noarch 1:0.241-512.el10 baseos 16 k perl-podlators noarch 1:5.01-511.el10 baseos 124 k perl-vars noarch 1.05-514.el10 appstream 14 k Transaction Summary ================================================================================ Install 81 Packages Total download size: 62 M Installed size: 183 M Downloading Packages: (1/81): htslib-1.23-1.el10.aarch64.rpm 4.1 MB/s | 560 kB 00:00 (2/81): groff-base-1.23.0-10.el10.aarch64.rpm 60 MB/s | 1.1 MB 00:00 (3/81): libatomic-14.3.1-4.2.el10.aarch64.rpm 14 MB/s | 58 kB 00:00 (4/81): make-4.4.1-9.el10.aarch64.rpm 74 MB/s | 585 kB 00:00 (5/81): ncurses-6.4-14.20240127.el10.aarch64.rp 75 MB/s | 421 kB 00:00 (6/81): perl-Carp-1.54-511.el10.noarch.rpm 10 MB/s | 30 kB 00:00 (7/81): htslib-tools-1.23-1.el10.aarch64.rpm 4.1 MB/s | 740 kB 00:00 (8/81): htslib-devel-1.23-1.el10.aarch64.rpm 602 kB/s | 107 kB 00:00 (9/81): perl-Data-Dumper-2.189-512.el10.aarch64 7.4 MB/s | 56 kB 00:00 (10/81): perl-Digest-1.20-511.el10.noarch.rpm 4.3 MB/s | 26 kB 00:00 (11/81): perl-Digest-MD5-2.59-6.el10.aarch64.rp 6.2 MB/s | 37 kB 00:00 (12/81): perl-Exporter-5.78-511.el10.noarch.rpm 13 MB/s | 32 kB 00:00 (13/81): perl-File-Temp-0.231.100-512.el10.noar 15 MB/s | 60 kB 00:00 (14/81): perl-Encode-3.21-511.el10.aarch64.rpm 134 MB/s | 1.1 MB 00:00 (15/81): perl-Getopt-Long-2.58-3.el10.noarch.rp 11 MB/s | 65 kB 00:00 (16/81): perl-HTTP-Tiny-0.088-512.el10.noarch.r 15 MB/s | 57 kB 00:00 (17/81): perl-IO-Socket-IP-0.42-512.el10.noarch 16 MB/s | 43 kB 00:00 (18/81): perl-MIME-Base64-3.16-511.el10.aarch64 12 MB/s | 31 kB 00:00 (19/81): perl-IO-Socket-SSL-2.085-3.el10.noarch 47 MB/s | 227 kB 00:00 (20/81): perl-Mozilla-CA-20231213-5.el10.noarch 5.5 MB/s | 15 kB 00:00 (21/81): perl-PathTools-3.91-512.el10.aarch64.r 23 MB/s | 85 kB 00:00 (22/81): perl-Pod-Escapes-1.07-511.el10.noarch. 8.2 MB/s | 21 kB 00:00 (23/81): perl-Pod-Perldoc-3.28.01-512.el10.noar 21 MB/s | 84 kB 00:00 (24/81): perl-Pod-Usage-2.03-511.el10.noarch.rp 14 MB/s | 41 kB 00:00 (25/81): perl-Pod-Simple-3.45-511.el10.noarch.r 48 MB/s | 218 kB 00:00 (26/81): perl-Socket-2.038-511.el10.aarch64.rpm 23 MB/s | 56 kB 00:00 (27/81): perl-Scalar-List-Utils-1.63-511.el10.a 15 MB/s | 73 kB 00:00 (28/81): perl-Storable-3.32-511.el10.aarch64.rp 25 MB/s | 98 kB 00:00 (29/81): perl-Term-ANSIColor-5.01-512.el10.noar 18 MB/s | 49 kB 00:00 (30/81): perl-Term-Cap-1.18-511.el10.noarch.rpm 6.6 MB/s | 23 kB 00:00 (31/81): perl-Text-ParseWords-3.31-511.el10.noa 6.7 MB/s | 17 kB 00:00 (32/81): perl-Text-Tabs+Wrap-2024.001-511.el10. 8.7 MB/s | 23 kB 00:00 (33/81): perl-Time-Local-1.350-511.el10.noarch. 16 MB/s | 35 kB 00:00 (34/81): perl-constant-1.33-512.el10.noarch.rpm 7.9 MB/s | 24 kB 00:00 (35/81): perl-URI-5.27-3.el10.noarch.rpm 31 MB/s | 134 kB 00:00 (36/81): perl-libnet-3.15-512.el10.noarch.rpm 29 MB/s | 127 kB 00:00 (37/81): perl-parent-0.241-512.el10.noarch.rpm 4.8 MB/s | 16 kB 00:00 (38/81): perl-podlators-5.01-511.el10.noarch.rp 32 MB/s | 124 kB 00:00 (39/81): annobin-docs-13.02-2.el10.noarch.rpm 23 MB/s | 87 kB 00:00 (40/81): cmake-filesystem-3.31.8-1.el10.aarch64 9.1 MB/s | 21 kB 00:00 (41/81): annobin-plugin-gcc-13.02-2.el10.aarch6 124 MB/s | 997 kB 00:00 (42/81): gcc-plugin-annobin-14.3.1-4.2.el10.aar 6.8 MB/s | 69 kB 00:00 (43/81): glibc-devel-2.39-99.el10.aarch64.rpm 30 MB/s | 589 kB 00:00 (44/81): cpp-14.3.1-4.2.el10.aarch64.rpm 217 MB/s | 11 MB 00:00 (45/81): kernel-headers-6.12.0-191.el10.aarch64 83 MB/s | 3.1 MB 00:00 (46/81): libasan-14.3.1-4.2.el10.aarch64.rpm 23 MB/s | 532 kB 00:00 (47/81): libmpc-1.3.1-7.el10.aarch64.rpm 6.8 MB/s | 73 kB 00:00 (48/81): libubsan-14.3.1-4.2.el10.aarch64.rpm 27 MB/s | 238 kB 00:00 (49/81): libxcrypt-devel-4.4.36-10.el10.aarch64 9.5 MB/s | 30 kB 00:00 (50/81): ncurses-c++-libs-6.4-14.20240127.el10. 14 MB/s | 40 kB 00:00 (51/81): perl-AutoLoader-5.74-514.el10.noarch.r 10 MB/s | 22 kB 00:00 (52/81): ncurses-devel-6.4-14.20240127.el10.aar 115 MB/s | 753 kB 00:00 (53/81): perl-B-1.89-514.el10.aarch64.rpm 33 MB/s | 179 kB 00:00 (54/81): perl-Class-Struct-0.68-514.el10.noarch 7.9 MB/s | 23 kB 00:00 (55/81): perl-DynaLoader-1.56-514.el10.aarch64. 10 MB/s | 27 kB 00:00 (56/81): perl-Errno-1.38-514.el10.aarch64.rpm 6.2 MB/s | 16 kB 00:00 (57/81): perl-Fcntl-1.18-514.el10.aarch64.rpm 12 MB/s | 30 kB 00:00 (58/81): perl-File-Basename-2.86-514.el10.noarc 3.1 MB/s | 18 kB 00:00 (59/81): perl-File-Path-2.18-512.el10.noarch.rp 7.5 MB/s | 35 kB 00:00 (60/81): perl-File-stat-1.14-514.el10.noarch.rp 2.2 MB/s | 18 kB 00:00 (61/81): perl-FileHandle-2.05-514.el10.noarch.r 1.9 MB/s | 16 kB 00:00 (62/81): perl-FindBin-1.54-514.el10.noarch.rpm 5.0 MB/s | 15 kB 00:00 (63/81): perl-Getopt-Std-1.14-514.el10.noarch.r 5.9 MB/s | 16 kB 00:00 (64/81): perl-IPC-Open3-1.22-514.el10.noarch.rp 8.0 MB/s | 23 kB 00:00 (65/81): perl-IO-1.55-514.el10.aarch64.rpm 18 MB/s | 81 kB 00:00 (66/81): perl-Net-SSLeay-1.94-8.el10.aarch64.rp 68 MB/s | 381 kB 00:00 (67/81): perl-POSIX-2.20-514.el10.aarch64.rpm 18 MB/s | 98 kB 00:00 (68/81): perl-SelectSaver-1.02-514.el10.noarch. 4.0 MB/s | 12 kB 00:00 (69/81): perl-Symbol-1.09-514.el10.noarch.rpm 4.9 MB/s | 15 kB 00:00 (70/81): perl-base-2.27-514.el10.noarch.rpm 4.2 MB/s | 17 kB 00:00 (71/81): perl-if-0.61.000-514.el10.noarch.rpm 3.7 MB/s | 15 kB 00:00 (72/81): perl-lib-0.65-514.el10.aarch64.rpm 4.8 MB/s | 16 kB 00:00 (73/81): perl-interpreter-5.40.2-514.el10.aarch 15 MB/s | 73 kB 00:00 (74/81): perl-locale-1.12-514.el10.noarch.rpm 2.3 MB/s | 14 kB 00:00 (75/81): perl-libs-5.40.2-514.el10.aarch64.rpm 193 MB/s | 2.3 MB 00:00 (76/81): perl-mro-1.29-514.el10.aarch64.rpm 5.8 MB/s | 30 kB 00:00 (77/81): perl-overload-1.37-514.el10.noarch.rpm 16 MB/s | 46 kB 00:00 (78/81): perl-overloading-0.02-514.el10.noarch. 4.1 MB/s | 14 kB 00:00 (79/81): perl-vars-1.05-514.el10.noarch.rpm 5.5 MB/s | 14 kB 00:00 (80/81): zlib-ng-compat-devel-2.2.3-3.el10.aarc 13 MB/s | 36 kB 00:00 (81/81): gcc-14.3.1-4.2.el10.aarch64.rpm 122 MB/s | 35 MB 00:00 -------------------------------------------------------------------------------- Total 98 MB/s | 62 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.3.1-7.el10.aarch64 1/81 Installing : htslib-1.23-1.el10.aarch64 2/81 Installing : cpp-14.3.1-4.2.el10.aarch64 3/81 Installing : ncurses-c++-libs-6.4-14.20240127.el10.aarch64 4/81 Installing : libubsan-14.3.1-4.2.el10.aarch64 5/81 Installing : libasan-14.3.1-4.2.el10.aarch64 6/81 Installing : kernel-headers-6.12.0-191.el10.aarch64 7/81 Installing : libxcrypt-devel-4.4.36-10.el10.aarch64 8/81 Installing : glibc-devel-2.39-99.el10.aarch64 9/81 Installing : cmake-filesystem-3.31.8-1.el10.aarch64 10/81 Installing : annobin-docs-13.02-2.el10.noarch 11/81 Installing : ncurses-6.4-14.20240127.el10.aarch64 12/81 Installing : make-1:4.4.1-9.el10.aarch64 13/81 Installing : libatomic-14.3.1-4.2.el10.aarch64 14/81 Installing : gcc-14.3.1-4.2.el10.aarch64 15/81 Running scriptlet: gcc-14.3.1-4.2.el10.aarch64 15/81 Running scriptlet: groff-base-1.23.0-10.el10.aarch64 16/81 Installing : groff-base-1.23.0-10.el10.aarch64 16/81 Running scriptlet: groff-base-1.23.0-10.el10.aarch64 16/81 Installing : perl-Digest-1.20-511.el10.noarch 17/81 Installing : perl-Digest-MD5-2.59-6.el10.aarch64 18/81 Installing : perl-B-1.89-514.el10.aarch64 19/81 Installing : perl-FileHandle-2.05-514.el10.noarch 20/81 Installing : perl-Data-Dumper-2.189-512.el10.aarch64 21/81 Installing : perl-libnet-3.15-512.el10.noarch 22/81 Installing : perl-AutoLoader-5.74-514.el10.noarch 23/81 Installing : perl-URI-5.27-3.el10.noarch 24/81 Installing : perl-Text-Tabs+Wrap-2024.001-511.el10.noarch 25/81 Installing : perl-Time-Local-2:1.350-511.el10.noarch 26/81 Installing : perl-Mozilla-CA-20231213-5.el10.noarch 27/81 Installing : perl-if-0.61.000-514.el10.noarch 28/81 Installing : perl-locale-1.12-514.el10.noarch 29/81 Installing : perl-IO-Socket-IP-0.42-512.el10.noarch 30/81 Installing : perl-Pod-Escapes-1:1.07-511.el10.noarch 31/81 Installing : perl-File-Path-2.18-512.el10.noarch 32/81 Installing : perl-IO-Socket-SSL-2.085-3.el10.noarch 33/81 Installing : perl-Net-SSLeay-1.94-8.el10.aarch64 34/81 Installing : perl-Term-ANSIColor-5.01-512.el10.noarch 35/81 Installing : perl-Class-Struct-0.68-514.el10.noarch 36/81 Installing : perl-POSIX-2.20-514.el10.aarch64 37/81 Installing : perl-IPC-Open3-1.22-514.el10.noarch 38/81 Installing : perl-Term-Cap-1.18-511.el10.noarch 39/81 Installing : perl-File-Temp-1:0.231.100-512.el10.noarch 40/81 Installing : perl-HTTP-Tiny-0.088-512.el10.noarch 41/81 Installing : perl-Pod-Simple-1:3.45-511.el10.noarch 42/81 Installing : perl-Socket-4:2.038-511.el10.aarch64 43/81 Installing : perl-SelectSaver-1.02-514.el10.noarch 44/81 Installing : perl-Symbol-1.09-514.el10.noarch 45/81 Installing : perl-File-stat-1.14-514.el10.noarch 46/81 Installing : perl-podlators-1:5.01-511.el10.noarch 47/81 Installing : perl-Pod-Perldoc-3.28.01-512.el10.noarch 48/81 Installing : perl-Text-ParseWords-3.31-511.el10.noarch 49/81 Installing : perl-Fcntl-1.18-514.el10.aarch64 50/81 Installing : perl-base-2.27-514.el10.noarch 51/81 Installing : perl-mro-1.29-514.el10.aarch64 52/81 Installing : perl-IO-1.55-514.el10.aarch64 53/81 Installing : perl-overloading-0.02-514.el10.noarch 54/81 Installing : perl-Pod-Usage-4:2.03-511.el10.noarch 55/81 Installing : perl-MIME-Base64-3.16-511.el10.aarch64 56/81 Installing : perl-Scalar-List-Utils-5:1.63-511.el10.aarch64 57/81 Installing : perl-constant-1.33-512.el10.noarch 58/81 Installing : perl-parent-1:0.241-512.el10.noarch 59/81 Installing : perl-Errno-1.38-514.el10.aarch64 60/81 Installing : perl-File-Basename-2.86-514.el10.noarch 61/81 Installing : perl-Getopt-Std-1.14-514.el10.noarch 62/81 Installing : perl-Storable-1:3.32-511.el10.aarch64 63/81 Installing : perl-overload-1.37-514.el10.noarch 64/81 Installing : perl-vars-1.05-514.el10.noarch 65/81 Installing : perl-Getopt-Long-1:2.58-3.el10.noarch 66/81 Installing : perl-Carp-1.54-511.el10.noarch 67/81 Installing : perl-Exporter-5.78-511.el10.noarch 68/81 Installing : perl-PathTools-3.91-512.el10.aarch64 69/81 Installing : perl-DynaLoader-1.56-514.el10.aarch64 70/81 Installing : perl-Encode-4:3.21-511.el10.aarch64 71/81 Installing : perl-libs-4:5.40.2-514.el10.aarch64 72/81 Installing : perl-interpreter-4:5.40.2-514.el10.aarch64 73/81 Installing : perl-FindBin-1.54-514.el10.noarch 74/81 Installing : perl-lib-0.65-514.el10.aarch64 75/81 Installing : annobin-plugin-gcc-13.02-2.el10.aarch64 76/81 Running scriptlet: annobin-plugin-gcc-13.02-2.el10.aarch64 76/81 Installing : gcc-plugin-annobin-14.3.1-4.2.el10.aarch64 77/81 Running scriptlet: gcc-plugin-annobin-14.3.1-4.2.el10.aarch64 77/81 Installing : zlib-ng-compat-devel-2.2.3-3.el10.aarch64 78/81 Installing : ncurses-devel-6.4-14.20240127.el10.aarch64 79/81 Installing : htslib-devel-1.23-1.el10.aarch64 80/81 Installing : htslib-tools-1.23-1.el10.aarch64 81/81 Running scriptlet: htslib-tools-1.23-1.el10.aarch64 81/81 Installed: annobin-docs-13.02-2.el10.noarch annobin-plugin-gcc-13.02-2.el10.aarch64 cmake-filesystem-3.31.8-1.el10.aarch64 cpp-14.3.1-4.2.el10.aarch64 gcc-14.3.1-4.2.el10.aarch64 gcc-plugin-annobin-14.3.1-4.2.el10.aarch64 glibc-devel-2.39-99.el10.aarch64 groff-base-1.23.0-10.el10.aarch64 htslib-1.23-1.el10.aarch64 htslib-devel-1.23-1.el10.aarch64 htslib-tools-1.23-1.el10.aarch64 kernel-headers-6.12.0-191.el10.aarch64 libasan-14.3.1-4.2.el10.aarch64 libatomic-14.3.1-4.2.el10.aarch64 libmpc-1.3.1-7.el10.aarch64 libubsan-14.3.1-4.2.el10.aarch64 libxcrypt-devel-4.4.36-10.el10.aarch64 make-1:4.4.1-9.el10.aarch64 ncurses-6.4-14.20240127.el10.aarch64 ncurses-c++-libs-6.4-14.20240127.el10.aarch64 ncurses-devel-6.4-14.20240127.el10.aarch64 perl-AutoLoader-5.74-514.el10.noarch perl-B-1.89-514.el10.aarch64 perl-Carp-1.54-511.el10.noarch perl-Class-Struct-0.68-514.el10.noarch perl-Data-Dumper-2.189-512.el10.aarch64 perl-Digest-1.20-511.el10.noarch perl-Digest-MD5-2.59-6.el10.aarch64 perl-DynaLoader-1.56-514.el10.aarch64 perl-Encode-4:3.21-511.el10.aarch64 perl-Errno-1.38-514.el10.aarch64 perl-Exporter-5.78-511.el10.noarch perl-Fcntl-1.18-514.el10.aarch64 perl-File-Basename-2.86-514.el10.noarch perl-File-Path-2.18-512.el10.noarch perl-File-Temp-1:0.231.100-512.el10.noarch perl-File-stat-1.14-514.el10.noarch perl-FileHandle-2.05-514.el10.noarch perl-FindBin-1.54-514.el10.noarch perl-Getopt-Long-1:2.58-3.el10.noarch perl-Getopt-Std-1.14-514.el10.noarch perl-HTTP-Tiny-0.088-512.el10.noarch perl-IO-1.55-514.el10.aarch64 perl-IO-Socket-IP-0.42-512.el10.noarch perl-IO-Socket-SSL-2.085-3.el10.noarch perl-IPC-Open3-1.22-514.el10.noarch perl-MIME-Base64-3.16-511.el10.aarch64 perl-Mozilla-CA-20231213-5.el10.noarch perl-Net-SSLeay-1.94-8.el10.aarch64 perl-POSIX-2.20-514.el10.aarch64 perl-PathTools-3.91-512.el10.aarch64 perl-Pod-Escapes-1:1.07-511.el10.noarch perl-Pod-Perldoc-3.28.01-512.el10.noarch perl-Pod-Simple-1:3.45-511.el10.noarch perl-Pod-Usage-4:2.03-511.el10.noarch perl-Scalar-List-Utils-5:1.63-511.el10.aarch64 perl-SelectSaver-1.02-514.el10.noarch perl-Socket-4:2.038-511.el10.aarch64 perl-Storable-1:3.32-511.el10.aarch64 perl-Symbol-1.09-514.el10.noarch perl-Term-ANSIColor-5.01-512.el10.noarch perl-Term-Cap-1.18-511.el10.noarch perl-Text-ParseWords-3.31-511.el10.noarch perl-Text-Tabs+Wrap-2024.001-511.el10.noarch perl-Time-Local-2:1.350-511.el10.noarch perl-URI-5.27-3.el10.noarch perl-base-2.27-514.el10.noarch perl-constant-1.33-512.el10.noarch perl-if-0.61.000-514.el10.noarch perl-interpreter-4:5.40.2-514.el10.aarch64 perl-lib-0.65-514.el10.aarch64 perl-libnet-3.15-512.el10.noarch perl-libs-4:5.40.2-514.el10.aarch64 perl-locale-1.12-514.el10.noarch perl-mro-1.29-514.el10.aarch64 perl-overload-1.37-514.el10.noarch perl-overloading-0.02-514.el10.noarch perl-parent-1:0.241-512.el10.noarch perl-podlators-1:5.01-511.el10.noarch perl-vars-1.05-514.el10.noarch zlib-ng-compat-devel-2.2.3-3.el10.aarch64 Complete! Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769040000 Wrote: /builddir/build/SRPMS/samtools-1.23-1.el10.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 3.6 kB/s | 1.5 kB 00:00 CentOS Stream 10 - BaseOS 120 kB/s | 5.5 kB 00:00 CentOS Stream 10 - AppStream 113 kB/s | 5.5 kB 00:00 CentOS Stream 10 - CRB 90 kB/s | 4.4 kB 00:00 CentOS Stream 10 - Extras packages 41 kB/s | 7.4 kB 00:00 Extra Packages for Enterprise Linux 10 - aarch6 171 kB/s | 22 kB 00:00 Package gcc-14.3.1-4.2.el10.aarch64 is already installed. Package htslib-devel-1.23-1.el10.aarch64 is already installed. Package htslib-tools-1.23-1.el10.aarch64 is already installed. Package make-1:4.4.1-9.el10.aarch64 is already installed. Package ncurses-devel-6.4-14.20240127.el10.aarch64 is already installed. Package perl-FindBin-1.54-514.el10.noarch is already installed. Package perl-Getopt-Long-1:2.58-3.el10.noarch is already installed. Package perl-lib-0.65-514.el10.aarch64 is already installed. Package perl-interpreter-4:5.40.2-514.el10.aarch64 is already installed. Package zlib-ng-compat-devel-2.2.3-3.el10.aarch64 is already installed. Dependencies resolved. Nothing to do. Complete! Finish: build setup for samtools-1.23-1.el10.src.rpm Start: rpmbuild samtools-1.23-1.el10.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769040000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.rfoIlP + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf samtools-1.23 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/samtools-1.23.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd samtools-1.23 + rm -rf /builddir/build/BUILD/samtools-1.23-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/samtools-1.23-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm -f INSTALL + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.Ayhk0J + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd samtools-1.23 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char $\*f$  = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed -r --in-place=.backup 's/^char $\*f$ ;/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 ;/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \$.*\$$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \$.*\$$/extern char \\1;/p'\''"#' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char $\*f$  = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char $\*f$ ;/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 ;/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \$.*\$$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \$.*\$$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./htslib-1.23/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./htslib-1.23/config.guess ++ basename ./htslib-1.23/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./htslib-1.23/config.guess '/usr/lib/rpm/redhat/config.guess' -> './htslib-1.23/config.guess' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./htslib-1.23/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./htslib-1.23/config.sub ++ basename ./htslib-1.23/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./htslib-1.23/config.sub '/usr/lib/rpm/redhat/config.sub' -> './htslib-1.23/config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=aarch64-redhat-linux --host=aarch64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection ' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --with-htslib=system checking for gawk... gawk checking for aarch64-redhat-linux-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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc option to enable large file support... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for NcursesW wide-character library... yes checking for working ncursesw/curses.h... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h + /usr/bin/make -O -j4 V=1 VERBOSE=1 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_aux.o bam_aux.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_index.o bam_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_cat.o bam_cat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_plcmd.o bam_plcmd.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_fastq.o bam_fastq.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_plbuf.o bam_plbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_md.o bam_md.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_view.o sam_view.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_reheader.o bam_reheader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_rmdupse.o bam_rmdupse.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_rmdup.o bam_rmdup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.23"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS ""' >> version.h echo '#define SAMTOOLS_CFLAGS "-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection "' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes "' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_stat.o bam_stat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam2bcf.o bam2bcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o cut_target.o cut_target.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_mate.o bam_mate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sample.o sample.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o coverage.o coverage.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam2depth.o bam2depth.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o padding.o padding.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o phase.o phase.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bedcov.o bedcov.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o dict.o dict.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bamshuf.o bamshuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o stats_isize.o stats_isize.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_flags.o bam_flags.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview.o bam_tview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_split.o bam_split.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_sort.o bam_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview_curses.o bam_tview_curses.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview_html.o bam_tview_html.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_quickcheck.o bam_quickcheck.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_lpileup.o bam_lpileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_addrprg.o bam_addrprg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o tmp_file.o tmp_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o stats.o stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_import.o bam_import.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_ampliconclip.o bam_ampliconclip.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_samples.o bam_samples.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o consensus_pileup.o consensus_pileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o amplicon_stats.o amplicon_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_markdup.o bam_markdup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o reference.o reference.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o reset.o reset.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o cram_size.o cram_size.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_opts.o sam_opts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_consensus.o bam_consensus.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_utils.o sam_utils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam.o bam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_checksum.o bam_checksum.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -DMAQ_LONGREADS -I. -I./lz4 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bedidx.o bedidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/md5fa.o misc/md5fa.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/ace2sam.o misc/ace2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/test.o test/test.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/wgsim.o misc/wgsim.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o lz4/lz4.o lz4/lz4.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bamtk.o bamtk.c ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o bam_checksum.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz -lpthread + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Qrn4oL + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64 ++ dirname /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd samtools-1.23 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/share/man/man1 /usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin /usr/bin/install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin /usr/bin/install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin /usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/share/man/man1 ++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/zoom2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/blast2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/bowtie2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/export2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/fasta-sanitize.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/interpolate_sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/novo2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/plot-ampliconstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/plot-bamstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/psl2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/sam2vcf.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/samtools.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/seq_cache_populate.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/soap2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/wgsim_eval.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/bin/zoom2sam.pl + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.23-1.el10 --unique-debug-suffix -1.23-1.el10.aarch64 --unique-debug-src-base samtools-1.23-1.el10.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.23 find-debuginfo: starting Extracting debug info from 7 files DWARF-compressing 7 files sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/samtools-1.23-1.el10.aarch64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.QbumPL + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd samtools-1.23 + ldd samtools + grep -E -e '/lib(64)?/libhts\.so\.' -e '/lib64/lp64d/libhts\.so\.' libhts.so.3 => /lib64/libhts.so.3 (0x0000ffffb9010000) + make test test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip= ${TEST_OPTS:-} test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok bgzip -c -b 65272 -s 5 /tmp/Ne3M9MD04u/bgzip.dat.gz .. ok bgzip -c -b 979200 -s 6 /tmp/Ne3M9MD04u/bgzip.dat.gz .. ok bgzip -c -b 652804 -s 6 /tmp/Ne3M9MD04u/bgzip.dat.gz .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/Ne3M9MD04u/faidx.fa 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/Ne3M9MD04u/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/Ne3M9MD04u/faidx.fa 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/Ne3M9MD04u/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/Ne3M9MD04u/faidx.fa 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/Ne3M9MD04u/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/Ne3M9MD04u/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/Ne3M9MD04u/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/Ne3M9MD04u/fqidx.fq 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/Ne3M9MD04u/fqidx.fq.gz 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/Ne3M9MD04u/fqidx.fq 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/Ne3M9MD04u/fqidx.fq.gz 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/Ne3M9MD04u/fqidx.fq 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/Ne3M9MD04u/fqidx.fq.gz 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/Ne3M9MD04u/fqidx.fq 1:99998-100007 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/Ne3M9MD04u/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /builddir/build/BUILD/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /builddir/build/BUILD/samtools-1.23/test/dat/dict.fa .. ok test_dict: /builddir/build/BUILD/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/Ne3M9MD04u/dict.fa.gz .. ok test_dict: cat /builddir/build/BUILD/samtools-1.23/test/dat/dict.fa | /builddir/build/BUILD/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /builddir/build/BUILD/samtools-1.23/samtools dict -AH < /builddir/build/BUILD/samtools-1.23/test/dat/dict.alias.fa .. ok test_dict: /builddir/build/BUILD/samtools-1.23/samtools dict -H -l /builddir/build/BUILD/samtools-1.23/test/dat/dict.alt < /builddir/build/BUILD/samtools-1.23/test/dat/dict.alias.fa .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view /tmp/Ne3M9MD04u/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view /tmp/Ne3M9MD04u/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/Ne3M9MD04u/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/Ne3M9MD04u/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools merge -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai /tmp/Ne3M9MD04u/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/Ne3M9MD04u/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam && cat /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -c /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam /tmp/Ne3M9MD04u/auto_indexed.csi && cat /tmp/Ne3M9MD04u/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.cram /tmp/Ne3M9MD04u/auto_indexed.crai && cat /tmp/Ne3M9MD04u/auto_indexed.crai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -c /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.sam /tmp/Ne3M9MD04u/auto_indexed.csi && cat /tmp/Ne3M9MD04u/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 /tmp/Ne3M9MD04u/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 /tmp/Ne3M9MD04u/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/Ne3M9MD04u/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/Ne3M9MD04u/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai /tmp/Ne3M9MD04u/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/Ne3M9MD04u/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -@ 2 -M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam && cat /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam /tmp/Ne3M9MD04u/auto_indexed.csi && cat /tmp/Ne3M9MD04u/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.cram /tmp/Ne3M9MD04u/auto_indexed.crai && cat /tmp/Ne3M9MD04u/auto_indexed.crai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.sam /tmp/Ne3M9MD04u/auto_indexed.csi && cat /tmp/Ne3M9MD04u/auto_indexed.csi .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/Ne3M9MD04u/mpileup.bam.list -f /tmp/Ne3M9MD04u/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/Ne3M9MD04u/mpileup.cram.list -f /tmp/Ne3M9MD04u/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/Ne3M9MD04u/mpileup.bam.urllist -f /tmp/Ne3M9MD04u/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/Ne3M9MD04u/mpileup.cram.urllist -f /tmp/Ne3M9MD04u/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/Ne3M9MD04u/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Ne3M9MD04u/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/Ne3M9MD04u/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Ne3M9MD04u/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup /builddir/build/BUILD/samtools-1.23/test/mpileup/overlap.bam | grep 128814202 test/test.pl: no IO::Pty module or can't open pty; skipping usage tests .. ok test_usage: samtools test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/Ne3M9MD04u/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/Ne3M9MD04u/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/Ne3M9MD04u/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/Ne3M9MD04u/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/Ne3M9MD04u/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/Ne3M9MD04u/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/Ne3M9MD04u/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/Ne3M9MD04u/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/Ne3M9MD04u/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/Ne3M9MD04u/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/Ne3M9MD04u/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/Ne3M9MD04u/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/Ne3M9MD04u/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/Ne3M9MD04u/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/Ne3M9MD04u/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/Ne3M9MD04u/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/Ne3M9MD04u/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/Ne3M9MD04u/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/Ne3M9MD04u/view.001.forn (SAM input) .. ok 68: Count -N /tmp/Ne3M9MD04u/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/Ne3M9MD04u/view.001.forn (BAM input) .. ok 70: Count -N /tmp/Ne3M9MD04u/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/Ne3M9MD04u/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/Ne3M9MD04u/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok 74: Count -d BC (SAM input) .. ok 75: Filter -d BC (BAM input) .. ok 76: Count -d BC (BAM input) .. ok 77: Filter -d BC (CRAM input) .. ok 78: Count -d BC (CRAM input) .. ok 79: Filter -d BC:TGCA (SAM input) .. ok 80: Count -d BC:TGCA (SAM input) .. ok 81: Filter -d BC:TGCA (BAM input) .. ok 82: Count -d BC:TGCA (BAM input) .. ok 83: Filter -d BC:TGCA (CRAM input) .. ok 84: Count -d BC:TGCA (CRAM input) .. ok 85: Filter -D BC:/tmp/Ne3M9MD04u/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/Ne3M9MD04u/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/Ne3M9MD04u/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/Ne3M9MD04u/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/Ne3M9MD04u/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/Ne3M9MD04u/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/Ne3M9MD04u/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/Ne3M9MD04u/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/Ne3M9MD04u/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/Ne3M9MD04u/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/Ne3M9MD04u/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/Ne3M9MD04u/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/Ne3M9MD04u/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/Ne3M9MD04u/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/Ne3M9MD04u/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/Ne3M9MD04u/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/Ne3M9MD04u/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/Ne3M9MD04u/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/Ne3M9MD04u/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/Ne3M9MD04u/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/Ne3M9MD04u/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/Ne3M9MD04u/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/Ne3M9MD04u/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/Ne3M9MD04u/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok 110: Count -d NE:TGCA (SAM input) .. ok 111: Filter -d NE:TGCA (BAM input) .. ok 112: Count -d NE:TGCA (BAM input) .. ok 113: Filter -d NE:TGCA (CRAM input) .. ok 114: Count -d NE:TGCA (CRAM input) .. ok 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/Ne3M9MD04u/view.test115.sam -h -d TGCA /tmp/Ne3M9MD04u/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -d TGCA /tmp/Ne3M9MD04u/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/Ne3M9MD04u/view.test117.sam -h -d TGCA /tmp/Ne3M9MD04u/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -d TGCA /tmp/Ne3M9MD04u/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/Ne3M9MD04u/view.test119.sam -h -d TGCA /tmp/Ne3M9MD04u/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -d TGCA /tmp/Ne3M9MD04u/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/Ne3M9MD04u/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Ne3M9MD04u/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/Ne3M9MD04u/view.test121.sam -h -D BClong:/tmp/Ne3M9MD04u/view.001.fobc /tmp/Ne3M9MD04u/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/Ne3M9MD04u/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Ne3M9MD04u/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/Ne3M9MD04u/view.001.fobc /tmp/Ne3M9MD04u/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/Ne3M9MD04u/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Ne3M9MD04u/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/Ne3M9MD04u/view.test123.sam -h -D BClong:/tmp/Ne3M9MD04u/view.001.fobc /tmp/Ne3M9MD04u/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/Ne3M9MD04u/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Ne3M9MD04u/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/Ne3M9MD04u/view.001.fobc /tmp/Ne3M9MD04u/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/Ne3M9MD04u/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Ne3M9MD04u/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/Ne3M9MD04u/view.test125.sam -h -D BClong:/tmp/Ne3M9MD04u/view.001.fobc /tmp/Ne3M9MD04u/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/Ne3M9MD04u/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Ne3M9MD04u/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/Ne3M9MD04u/view.001.fobc /tmp/Ne3M9MD04u/view.test006.cram --no-PG .. expected failure 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/Ne3M9MD04u/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/Ne3M9MD04u/view.001.sam --no-PG .. expected failure 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/Ne3M9MD04u/view.001.sam --no-PG .. expected failure 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/Ne3M9MD04u/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/Ne3M9MD04u/view.test001.bam --no-PG .. expected failure 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/Ne3M9MD04u/view.test001.bam --no-PG .. expected failure 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/Ne3M9MD04u/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/Ne3M9MD04u/view.test006.cram --no-PG .. expected failure 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/Ne3M9MD04u/view.test006.cram --no-PG .. expected failure 133: Filter -d NM:13 (SAM input) .. ok 134: Count -d NM:13 (SAM input) .. ok 135: Filter -d NM:13 (BAM input) .. ok 136: Count -d NM:13 (BAM input) .. ok 137: Filter -d NM:13 (CRAM input) .. ok 138: Count -d NM:13 (CRAM input) .. ok 139: Filter -d ab:z (SAM input) .. ok 140: Count -d ab:z (SAM input) .. ok 141: Filter -d ab:z (BAM input) .. ok 142: Count -d ab:z (BAM input) .. ok 143: Filter -d ab:z (CRAM input) .. ok 144: Count -d ab:z (CRAM input) .. ok 145: Filter -l Library 2 (SAM input) .. ok 146: Count -l Library 2 (SAM input) .. ok 147: Filter -l Library 2 (BAM input) .. ok 148: Count -l Library 2 (BAM input) .. ok 149: Filter -l Library 2 (CRAM input) .. ok 150: Count -l Library 2 (CRAM input) .. ok 151: Filter -l Library 3 (SAM input) .. ok 152: Count -l Library 3 (SAM input) .. ok 153: Filter -l Library 3 (BAM input) .. ok 154: Count -l Library 3 (BAM input) .. ok 155: Filter -l Library 3 (CRAM input) .. ok 156: Count -l Library 3 (CRAM input) .. ok 157: Filter -q 50 (SAM input) .. ok 158: Count -q 50 (SAM input) .. ok 159: Filter -q 50 (BAM input) .. ok 160: Count -q 50 (BAM input) .. ok 161: Filter -q 50 (CRAM input) .. ok 162: Count -q 50 (CRAM input) .. ok 163: Filter -q 99 (SAM input) .. ok 164: Count -q 99 (SAM input) .. ok 165: Filter -q 99 (BAM input) .. ok 166: Count -q 99 (BAM input) .. ok 167: Filter -q 99 (CRAM input) .. ok 168: Count -q 99 (CRAM input) .. ok 169: Filter -q 100 (SAM input) .. ok 170: Count -q 100 (SAM input) .. ok 171: Filter -q 100 (BAM input) .. ok 172: Count -q 100 (BAM input) .. ok 173: Filter -q 100 (CRAM input) .. ok 174: Count -q 100 (CRAM input) .. ok 175: Filter -x fa (SAM input) .. ok 176: Count -x fa (SAM input) .. ok 177: Filter -x fa (BAM input) .. ok 178: Count -x fa (BAM input) .. ok 179: Filter -x fa (CRAM input) .. ok 180: Count -x fa (CRAM input) .. ok 181: Filter -x fa -x ha (SAM input) .. ok 182: Count -x fa -x ha (SAM input) .. ok 183: Filter -x fa -x ha (BAM input) .. ok 184: Count -x fa -x ha (BAM input) .. ok 185: Filter -x fa -x ha (CRAM input) .. ok 186: Count -x fa -x ha (CRAM input) .. ok 187: Filter -x fa,ha (SAM input) .. ok 188: Count -x fa,ha (SAM input) .. ok 189: Filter -x fa,ha (BAM input) .. ok 190: Count -x fa,ha (BAM input) .. ok 191: Filter -x fa,ha (CRAM input) .. ok 192: Count -x fa,ha (CRAM input) .. ok 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 205: Filter -x fa -r grp2 (SAM input) .. ok 206: Count -x fa -r grp2 (SAM input) .. ok 207: Filter -x fa -r grp2 (BAM input) .. ok 208: Count -x fa -r grp2 (BAM input) .. ok 209: Filter -x fa -r grp2 (CRAM input) .. ok 210: Count -x fa -r grp2 (CRAM input) .. ok 211: Filter -x RG -r grp2 (SAM input) .. ok 212: Count -x RG -r grp2 (SAM input) .. ok 213: Filter -x RG -r grp2 (BAM input) .. ok 214: Count -x RG -r grp2 (BAM input) .. ok 215: Filter -x RG -r grp2 (CRAM input) .. ok 216: Count -x RG -r grp2 (CRAM input) .. ok 217: Filter -m 10 (SAM input) .. ok 218: Count -m 10 (SAM input) .. ok 219: Filter -m 10 (BAM input) .. ok 220: Count -m 10 (BAM input) .. ok 221: Filter -m 10 (CRAM input) .. ok 222: Count -m 10 (CRAM input) .. ok 223: Filter -m 11 (SAM input) .. ok 224: Count -m 11 (SAM input) .. ok 225: Filter -m 11 (BAM input) .. ok 226: Count -m 11 (BAM input) .. ok 227: Filter -m 11 (CRAM input) .. ok 228: Count -m 11 (CRAM input) .. ok 229: Filter -m 15 (SAM input) .. ok 230: Count -m 15 (SAM input) .. ok 231: Filter -m 15 (BAM input) .. ok 232: Count -m 15 (BAM input) .. ok 233: Filter -m 15 (CRAM input) .. ok 234: Count -m 15 (CRAM input) .. ok 235: Filter -m 16 (SAM input) .. ok 236: Count -m 16 (SAM input) .. ok 237: Filter -m 16 (BAM input) .. ok 238: Count -m 16 (BAM input) .. ok 239: Filter -m 16 (CRAM input) .. ok 240: Count -m 16 (CRAM input) .. ok 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 247: Filter -e [BC] (SAM input) .. ok 248: Count -e [BC] (SAM input) .. ok 249: Filter -e [BC] (BAM input) .. ok 250: Count -e [BC] (BAM input) .. ok 251: Filter -e [BC] (CRAM input) .. ok 252: Count -e [BC] (CRAM input) .. ok 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 259: Filter -e mapq >= 50 (SAM input) .. ok 260: Count -e mapq >= 50 (SAM input) .. ok 261: Filter -e mapq >= 50 (BAM input) .. ok 262: Count -e mapq >= 50 (BAM input) .. ok 263: Filter -e mapq >= 50 (CRAM input) .. ok 264: Count -e mapq >= 50 (CRAM input) .. ok 265: Filter -e mapq >= 99 (SAM input) .. ok 266: Count -e mapq >= 99 (SAM input) .. ok 267: Filter -e mapq >= 99 (BAM input) .. ok 268: Count -e mapq >= 99 (BAM input) .. ok 269: Filter -e mapq >= 99 (CRAM input) .. ok 270: Count -e mapq >= 99 (CRAM input) .. ok 271: Filter -e mapq >= 100 (SAM input) .. ok 272: Count -e mapq >= 100 (SAM input) .. ok 273: Filter -e mapq >= 100 (BAM input) .. ok 274: Count -e mapq >= 100 (BAM input) .. ok 275: Filter -e mapq >= 100 (CRAM input) .. ok 276: Count -e mapq >= 100 (CRAM input) .. ok 277: 1bp reads file SAM -> BAM -> SAM .. ok 278: 1bp reads file SAM -> CRAM -> SAM .. ok 278: Region Z (BAM input) .. ok 279: Count Z (BAM input) .. ok 280: Region Z (CRAM input) .. ok 281: Count Z (CRAM input) .. ok 282: Region Z:30 (BAM input) .. ok 283: Count Z:30 (BAM input) .. ok 284: Region Z:30 (CRAM input) .. ok 285: Count Z:30 (CRAM input) .. ok 286: Region Z:20-40 (BAM input) .. ok 287: Count Z:20-40 (BAM input) .. ok 288: Region Z:20-40 (CRAM input) .. ok 289: Count Z:20-40 (CRAM input) .. ok 290: Region ref1 (BAM input) .. ok 291: Count ref1 (BAM input) .. ok 292: Region ref1 (CRAM input) .. ok 293: Count ref1 (CRAM input) .. ok 294: Region ref1:15 (BAM input) .. ok 295: Count ref1:15 (BAM input) .. ok 296: Region ref1:15 (CRAM input) .. ok 297: Count ref1:15 (CRAM input) .. ok 298: Region ref1:15-45 (BAM input) .. ok 299: Count ref1:15-45 (BAM input) .. ok 300: Region ref1:15-45 (CRAM input) .. ok 301: Count ref1:15-45 (CRAM input) .. ok 302: Region ref1:15-45 ref2 (BAM input) .. ok 303: Count ref1:15-45 ref2 (BAM input) .. ok 304: Region ref1:15-45 ref2 (CRAM input) .. ok 305: Count ref1:15-45 ref2 (CRAM input) .. ok 306: Region ref1:15-45 ref2:16 (BAM input) .. ok 307: Count ref1:15-45 ref2:16 (BAM input) .. ok 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 318: Region -f 128 ref1 (BAM input) .. ok 319: Count -f 128 ref1 (BAM input) .. ok 320: Region -f 128 ref1 (CRAM input) .. ok 321: Count -f 128 ref1 (CRAM input) .. ok 322: Region -q 50 ref1:15-45 (BAM input) .. ok 323: Count -q 50 ref1:15-45 (BAM input) .. ok 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 326: Region -r grp2 ref1:15-45 (BAM input) .. ok 327: Count -r grp2 ref1:15-45 (BAM input) .. ok 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok 330: Region * (BAM input) .. ok 331: Count * (BAM input) .. ok 332: Region * (CRAM input) .. ok 333: Count * (CRAM input) .. ok 334: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.03.bed (BAM input).. ok 351: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.03.bed (BAM input).. ok 352: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.03.bed (CRAM input).. ok 353: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.03.bed (CRAM input).. ok 354: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z (BAM input).. ok 355: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z (BAM input).. ok 356: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z (CRAM input).. ok 357: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z (CRAM input).. ok 358: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:30 (BAM input).. ok 359: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:30 (BAM input).. ok 360: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 361: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 362: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 363: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 364: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 365: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 366: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 367: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 368: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 369: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 370: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 371: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 372: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 373: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 374: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref2 (BAM input).. ok 375: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref2 (BAM input).. ok 376: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref2 (CRAM input).. ok 377: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref2 (CRAM input).. ok 378: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 379: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 380: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 381: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 382: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 383: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 384: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 385: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 386: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -f 128 (BAM input).. ok 387: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -f 128 (BAM input).. ok 388: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 389: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 390: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -q 5 (BAM input).. ok 391: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -q 5 (BAM input).. ok 392: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 393: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 394: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 395: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 396: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 397: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 398: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 399: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 400: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 401: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 402: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 403: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 404: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 405: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 406: -L with nested regions .. ok 407: Make BAM with no M5/UR tags .. ok 408: Add @SQ with -t (SAM -> SAM) .. ok 409: Add @SQ with -T (SAM -> SAM) .. ok 410: Add @SQ with -t (BAM -> SAM) .. ok 411: Add @SQ with -T (BAM -> SAM) .. ok 412: Add @SQ with -t (SAM -> BAM) .. ok 413: Add @SQ with -T (SAM -> BAM) .. ok 414: Add @SQ with -t (BAM -> BAM) .. ok 415: Add @SQ with -T (BAM -> BAM) .. ok 416: Add @SQ with -t (SAM -> CRAM) .. ok 417: Add @SQ with -T (SAM -> CRAM) .. ok 418: Add @SQ with -t (BAM -> CRAM) .. ok 419: Add @SQ with -T (BAM -> CRAM) .. ok 420: Make CRAM with no UR field .. ok 421: Decoding CRAM with no UR field via -T .. ok 422: CIGAR B-operator removal .. ok 423: Big SAM -> BAM .. ok 424: Big SAM -> BAM (2 threads) .. ok 425: Big SAM -> BAM (4 threads) .. ok 426: Big SAM -> CRAM .. ok 427: Big SAM -> CRAM (2 threads) .. ok 428: Big SAM -> CRAM (4 threads) .. ok 429: Subsample 0.2 (SAM input) ............ ok 430: Subsample 0.5 (SAM input) ............ ok 431: Subsample 0.8 (SAM input) ............ ok 432: Subsample 0.2 (BAM input) ............ ok 433: Subsample 0.5 (BAM input) ............ ok 434: Subsample 0.8 (BAM input) ............ ok 435: Subsample 0.2 (CRAM input) ............ ok 436: Subsample 0.5 (CRAM input) ............ ok 437: Subsample 0.8 (CRAM input) ............ ok 438: SAM add PG .. ok 439: Unset dup flag, remove dt and do tags .. ok 440: Unmap dup flagged reads. .. ok 441: Unmap dup flagged reads. .. ok 442: fetch pairs .. ok 443: fetch pairs .. ok 444: fetch pairs .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -h 0 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -h 1 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -h 5 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -h 29 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -h 30 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -n 0 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -n 1 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -n 5 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -h 5 -n 5 < /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate BAM region file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate BAM region file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate BAM region file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate BAM region file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat CRAM subregion files .. ok 5: cat BAM files to stdout .. ok 6: cat recompressed BAM files to stdout .. ok 7: cat CRAM files to stdout .. ok 8: cat CRAM subregion files to stdout .. ok 9: cat CRAM part 1/2 .. ok 9: cat CRAM part 2/2 .. ok 9: cat CRAM parts 1/2 + 2/2 .. ok 10: cat BAM files with new header .. ok 11: cat recompressed BAM files with new header .. ok 12: cat CRAM files with new header .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -0 /builddir/build/BUILD/samtools-1.23/test/0.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -0 /builddir/build/BUILD/samtools-1.23/test/0.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -s /builddir/build/BUILD/samtools-1.23/test/s.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T RG,BC,QT -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T RG,BC,QT,MD,ia -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/2.interleaved.fq -T "" .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/3.interleaved.fq -i .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/4.aux.fq -T "*" .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/4.aux.fq -T "" .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -U test/bam2fq/UMI.fq.expected .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -U --UMI-tag OX test/bam2fq/UMI.fq.expected .. ok test_bam2fq: Generate BAM file .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.23/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -t -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.703.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.23/test/o.fq -2 /builddir/build/BUILD/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fasta -N -1 /builddir/build/BUILD/samtools-1.23/test/o.fa -2 /builddir/build/BUILD/samtools-1.23/test/o.fa /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -o /builddir/build/BUILD/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -s /tmp/Ne3M9MD04u/bam2fq.discard.s.fq -0 /tmp/Ne3M9MD04u/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.013.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.23/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.23/test/i2.fq -0 /builddir/build/BUILD/samtools-1.23/test/0.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.014.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T '' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -t -T '*' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T '*' -d MD:10 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T '*' -d NM:0 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T '*' -d ia /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -d NM:13 -d NM:14 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -D NM:test/dat/bam2fq.NM-D /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -D MD:test/dat/bam2fq.MD-D /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -O --no-sc --no-sc-bkp -T 's0' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -O --no-sc -T's0' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -O --no-sc /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -O --no-sc --sc-aux s1 -T's0,s1' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -U test/import/UMI.expected.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -U --UMI-tag RX,OX test/import/UMI-OX.expected.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.23/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -t -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.703.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -1 /builddir/build/BUILD/samtools-1.23/test/o.fq -2 /builddir/build/BUILD/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fasta -@ 2 -N -1 /builddir/build/BUILD/samtools-1.23/test/o.fa -2 /builddir/build/BUILD/samtools-1.23/test/o.fa /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -o /builddir/build/BUILD/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -s /tmp/Ne3M9MD04u/bam2fq.discard.s.fq -0 /tmp/Ne3M9MD04u/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.013.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.23/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.23/test/i2.fq -0 /builddir/build/BUILD/samtools-1.23/test/0.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.014.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -T '' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -t -T '*' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -T '*' -d MD:10 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -T '*' -d NM:0 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -T '*' -d ia /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -d NM:13 -d NM:14 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -O --no-sc --no-sc-bkp -T 's0' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -O --no-sc -T's0' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -O --no-sc /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -O --no-sc --sc-aux s1 -T's0,s1' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -U test/import/UMI.expected.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -U --UMI-tag RX,OX test/import/UMI-OX.expected.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa -i 0 /builddir/build/BUILD/samtools-1.23/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -t /builddir/build/BUILD/samtools-1.23/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -g 4 -t /builddir/build/BUILD/samtools-1.23/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -g 4 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.23/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.23/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.23/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.23/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /builddir/build/BUILD/samtools-1.23/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /builddir/build/BUILD/samtools-1.23/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /builddir/build/BUILD/samtools-1.23/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -I s1 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -I grp2 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -I grp3 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -I Sample /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/mpileup/ce.fa /builddir/build/BUILD/samtools-1.23/test/stat/15.big_del.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam | grep -e"^RFS" .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa ERR: [E::faidx_adjust_position] The sequence "ref1" was not found Failed to fetch the sequence "ref1" .. expected failure test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa | grep -e"^RFS" .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats --ref-stats-chunk -1 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa | grep -e"^RFS" .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa alpha:10-20 | grep -e"^RFS" .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa -t /builddir/build/BUILD/samtools-1.23/test/stat/11.stats.targets | grep -e"^RFS" .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa -t /builddir/build/BUILD/samtools-1.23/test/stat/11.stats.targets ref1 | grep -e"^RFS" .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam -b /tmp/FejNvyhTzf - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/Ne3M9MD04u/merge.tag.1.bam /tmp/Ne3M9MD04u/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/Ne3M9MD04u/merge.tag.3.bam /tmp/Ne3M9MD04u/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge --no-PG -O SAM - /builddir/build/BUILD/samtools-1.23/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.23/test/merge/merge.bed - /tmp/Ne3M9MD04u/merge.bed.1.bam /tmp/Ne3M9MD04u/merge.bed.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge --no-PG -r -O SAM - /builddir/build/BUILD/samtools-1.23/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge --no-PG -O SAM --template-coordinate - /builddir/build/BUILD/samtools-1.23/test/merge/test_template_coordinate.1.sam /builddir/build/BUILD/samtools-1.23/test/merge/test_template_coordinate.2.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam -b /tmp/lRMRl2pJyR - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/Ne3M9MD04u/merge.tag.1.bam /tmp/Ne3M9MD04u/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/Ne3M9MD04u/merge.tag.3.bam /tmp/Ne3M9MD04u/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM - /builddir/build/BUILD/samtools-1.23/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.23/test/merge/merge.bed - /tmp/Ne3M9MD04u/merge.bed.1.bam /tmp/Ne3M9MD04u/merge.bed.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 --no-PG -r -O SAM - /builddir/build/BUILD/samtools-1.23/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /builddir/build/BUILD/samtools-1.23/test/merge/test_template_coordinate.1.sam /builddir/build/BUILD/samtools-1.23/test/merge/test_template_coordinate.2.sam .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/Ne3M9MD04u/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -f /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/Ne3M9MD04u/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -o /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/Ne3M9MD04u/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -N -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -t RG -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -n -t RG -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -t AS -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -t FI -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort --template-coordinate -m 10M /builddir/build/BUILD/samtools-1.23/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -m 10M -M -K10 -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -m 10M -M -K10 -I /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -m 10M -MH -K10 -I /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/Ne3M9MD04u/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/Ne3M9MD04u/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/Ne3M9MD04u/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -N -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -t RG -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -n -t RG -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -t AS -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -t FI -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 --template-coordinate -m 10M /builddir/build/BUILD/samtools-1.23/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -m 10M -M -K10 -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -m 10M -M -K10 -I /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -m 10M -MH -K10 -I /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate --output-fmt=sam -O /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -o /builddir/build/BUILD/samtools-1.23/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -o /builddir/build/BUILD/samtools-1.23/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate --output-fmt=sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate --output-fmt=sam -f /builddir/build/BUILD/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 --output-fmt=sam -O /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.23/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.23/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 --output-fmt=sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 --output-fmt=sam -f /builddir/build/BUILD/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.23/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.23/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/sanitize.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_draft.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_bounds.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.23/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.23/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/sanitize.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_draft.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_bounds.sam - .. ok /builddir/build/BUILD/samtools-1.23/samtools calmd -uAr /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa .. ok /builddir/build/BUILD/samtools-1.23/samtools calmd -@ 2 -uAr /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa .. ok test_idxstat: /builddir/build/BUILD/samtools-1.23/samtools idxstats /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam .. ok test_idxstat: /builddir/build/BUILD/samtools-1.23/samtools idxstats /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.cram .. ok test_idxstat: /builddir/build/BUILD/samtools-1.23/samtools idxstats /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck -v /builddir/build/BUILD/samtools-1.23/test/quickcheck/1.quickcheck.badeof.bam /builddir/build/BUILD/samtools-1.23/test/quickcheck/2.quickcheck.badheader.bam /builddir/build/BUILD/samtools-1.23/test/quickcheck/3.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.23/test/quickcheck/4.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.23/test/quickcheck/5.quickcheck.scramble30.truncated.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/6.quickcheck.cram21.ok.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/7.quickcheck.cram30.ok.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/8.quickcheck.cram21.truncated.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/9.quickcheck.cram30.truncated.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck -uv /builddir/build/BUILD/samtools-1.23/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v21.cram | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader --in-place /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v21.cram && /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader --in-place /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v30.cram && /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -m orphan_only /builddir/build/BUILD/samtools-1.23/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -R '1#9' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.23/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.23/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -m orphan_only /builddir/build/BUILD/samtools-1.23/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -R '1#9' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.23/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.23/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/3_missing_mc.sam - ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. samtools markdup: error, unable to assign pair hash key. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/4_missing_ms.sam - ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -O sam -r --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/8_optical_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.23/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.23/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/17_read_group.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /builddir/build/BUILD/samtools-1.23/test/markdup/18_primary_duplicate_count.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/3_missing_mc.sam - ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. samtools markdup: error, unable to assign pair hash key. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/4_missing_ms.sam - ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam -r --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/8_optical_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.23/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.23/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/17_read_group.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /builddir/build/BUILD/samtools-1.23/test/markdup/18_primary_duplicate_count.sam - .. ok test_bedcov: /builddir/build/BUILD/samtools-1.23/samtools bedcov /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.23/samtools bedcov -j /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.23/samtools bedcov -g512 -G2048 /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.23/samtools bedcov -c /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bam .. ok .. ok .. ok .. ok .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -p 5 -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -d RG -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -d an -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -d an -M 3 -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.unk.sam /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools sort -t nn /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam | /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam - .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -p 5 -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -d RG -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -d an -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.unk.sam /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -t nn /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam | /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam - .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /tmp/Ne3M9MD04u/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /tmp/Ne3M9MD04u/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG -L /builddir/build/BUILD/samtools-1.23/test/large_pos/test.bed /tmp/Ne3M9MD04u/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools sort -O sam --no-PG -m 10M /builddir/build/BUILD/samtools-1.23/test/large_pos/longref_name.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools merge -O sam --no-PG - /builddir/build/BUILD/samtools-1.23/test/large_pos/longref.sam /builddir/build/BUILD/samtools-1.23/test/large_pos/longref2.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools depth /builddir/build/BUILD/samtools-1.23/test/large_pos/longref.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools depth -b /builddir/build/BUILD/samtools-1.23/test/large_pos/test.bed /builddir/build/BUILD/samtools-1.23/test/large_pos/longref.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/Ne3M9MD04u/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam --no-PG - - | /builddir/build/BUILD/samtools-1.23/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test2.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test2.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.23/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_hard_clipped.expected.sam /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_soft_clipped.expected.sam /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_soft_clipped_strand.expected.sam /builddir/build/BUILD/samtools-1.23/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.23/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.23/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag | /builddir/build/BUILD/samtools-1.23/samtools view .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag < /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23/samtools view .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23/samtools view .. ok test_reset: cat /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.cram .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG sam_to_fixed_bam /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index --no-PG /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam -e"@PG" .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/reset/seq.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset /builddir/build/BUILD/samtools-1.23/test/reset/seq.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum /builddir/build/BUILD/samtools-1.23/test/checksum/chk1.bam | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -a /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -qv /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -qv -a /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -m /builddir/build/BUILD/samtools-1.23/test/checksum/chk1-ERR*.tmp.chk | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -m /builddir/build/BUILD/samtools-1.23/test/checksum/chk2-*.tmp.chk | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 /builddir/build/BUILD/samtools-1.23/test/checksum/chk1.bam | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -a /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -qv /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -qv -a /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -m /builddir/build/BUILD/samtools-1.23/test/checksum/chk1-ERR*.tmp.chk | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -m /builddir/build/BUILD/samtools-1.23/test/checksum/chk2-*.tmp.chk | sed 's/$# Checksum[^:]*:$.*/\1/' .. ok test_coverage: /builddir/build/BUILD/samtools-1.23/samtools coverage /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam .. ok test_coverage: /builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 1 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam .. ok test_coverage: /builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 2 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam .. ok test_coverage: /builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 2 -Q 8 -q 45 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam .. ok test_coverage: /builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 1 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam /tmp/Ne3M9MD04u/sample1.sam .. ok test_coverage: /builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 4 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam /tmp/Ne3M9MD04u/sample1.sam .. ok Number of tests: total .. 998 passed .. 966 failed .. 0 expected failure .. 32 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="gawk" ../regression.sh mpileup.reg === Testing mpileup.reg regressions === [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 120 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="gawk" ../regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 55 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="gawk" ../regression.sh cram-size.reg === Testing cram-size.reg regressions === Expected passes: 5 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/consensus && AWK="gawk" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 77 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/consensus && AWK="gawk" PARAM="-@4 -Z4" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 77 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/cram_size && AWK="gawk" ../regression.sh cram_size.reg === Testing cram_size.reg regressions === Expected passes: 3 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS + RPM_EC=0 ++ jobs -p + exit 0 Processing files: samtools-1.23-1.el10.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.4wnZ7U + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + DOCDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/share/doc/samtools + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/share/doc/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/AUTHORS /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/share/doc/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/ChangeLog.old /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/share/doc/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/NEWS.md /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/share/doc/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/examples /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/share/doc/samtools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.rNbM5X + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/share/licenses/samtools + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/share/licenses/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/LICENSE /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64/usr/share/licenses/samtools + RPM_EC=0 ++ jobs -p + exit 0 Provides: samtools = 1.23-1.el10 samtools(aarch-64) = 1.23-1.el10 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.1)(64bit) libhts.so.3(HTSLIB_1.10)(64bit) libhts.so.3(HTSLIB_1.11)(64bit) libhts.so.3(HTSLIB_1.12)(64bit) libhts.so.3(HTSLIB_1.14)(64bit) libhts.so.3(HTSLIB_1.15)(64bit) libhts.so.3(HTSLIB_1.16)(64bit) libhts.so.3(HTSLIB_1.17)(64bit) libhts.so.3(HTSLIB_1.18)(64bit) libhts.so.3(HTSLIB_1.2.1)(64bit) libhts.so.3(HTSLIB_1.21)(64bit) libhts.so.3(HTSLIB_1.22)(64bit) libhts.so.3(HTSLIB_1.23)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) libhts.so.3(HTSLIB_1.9)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: samtools-debugsource-1.23-1.el10.aarch64 Provides: samtools-debugsource = 1.23-1.el10 samtools-debugsource(aarch-64) = 1.23-1.el10 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: samtools-debuginfo-1.23-1.el10.aarch64 Provides: debuginfo(build-id) = 3f3722e8b5cce95d02ee028221ffe0ce210932af debuginfo(build-id) = 6765850b6185e6f5cb110c01cbf750d448eac23a debuginfo(build-id) = 9694de5e6d2ad6ade6b6d6c7a245ddfeea11c05b debuginfo(build-id) = 979e52b3b5c46155a486d594b12ab7c1b7970eba debuginfo(build-id) = d9c9c85002e68fa5c8f4965c0ca1c862b276a1ac debuginfo(build-id) = ee50b6da3c5e2e7ec9ecaf6345587cb112bfac54 debuginfo(build-id) = fa7cd4b2bc5067491370e6c33b0126cbe4228f2e samtools-debuginfo = 1.23-1.el10 samtools-debuginfo(aarch-64) = 1.23-1.el10 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: samtools-debugsource(aarch-64) = 1.23-1.el10 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64 Wrote: /builddir/build/RPMS/samtools-1.23-1.el10.aarch64.rpm Wrote: /builddir/build/RPMS/samtools-debugsource-1.23-1.el10.aarch64.rpm Wrote: /builddir/build/RPMS/samtools-debuginfo-1.23-1.el10.aarch64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.VYeqdH + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.23-1.el10.aarch64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.AvvtVE + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/samtools-1.23-SPECPARTS + rm -rf samtools-1.23 samtools-1.23.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild samtools-1.23-1.el10.src.rpm Finish: build phase for samtools-1.23-1.el10.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/centos-stream+epel-10-aarch64-1769501805.999475/root/var/log/dnf.rpm.log /var/lib/mock/centos-stream+epel-10-aarch64-1769501805.999475/root/var/log/dnf.librepo.log /var/lib/mock/centos-stream+epel-10-aarch64-1769501805.999475/root/var/log/dnf.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/samtools-1.23-1.el10.src.rpm) Config(child) 1 minutes 3 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "samtools-debugsource", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "aarch64" }, { "name": "samtools", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "aarch64" }, { "name": "samtools", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "src" }, { "name": "samtools-debuginfo", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "aarch64" } ] } RPMResults finished