Warning: Permanently added '13.221.252.70' (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-x86_64 --chroot epel-10-x86_64 Version: 1.6 PID: 23076 Logging PID: 23078 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 10066101, 'buildroot_pkgs': [], 'chroot': 'epel-10-x86_64', '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-x86_64/', '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-x86_64', '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-05b8sndb/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-05b8sndb/samtools', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-05b8sndb/samtools'... Running: git checkout 7afd4b414b02c829eb5656fa17d98633a259ea94 -- cmd: ['git', 'checkout', '7afd4b414b02c829eb5656fa17d98633a259ea94', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-05b8sndb/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-05b8sndb/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 208M 0 --:--:-- --:--:-- --:--:-- 212M 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-05b8sndb/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-05b8sndb/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769501915.991329 -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-05b8sndb/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-05b8sndb/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769501915.991329 -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-05b8sndb/samtools/samtools.spec) Config(centos-stream+epel-10-x86_64) 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-x86_64-bootstrap-1769501915.991329/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-a073855e-7605-4239-a88f-1b000e61a1b1 INFO: Checking that eee3feca625505a534e2f5b3e36aae2f6c3e3e929f8b5a4701e335a06a83735e image matches host's architecture INFO: Copy content of container eee3feca625505a534e2f5b3e36aae2f6c3e3e929f8b5a4701e335a06a83735e to /var/lib/mock/centos-stream+epel-10-x86_64-bootstrap-1769501915.991329/root INFO: mounting eee3feca625505a534e2f5b3e36aae2f6c3e3e929f8b5a4701e335a06a83735e with podman image mount INFO: image eee3feca625505a534e2f5b3e36aae2f6c3e3e929f8b5a4701e335a06a83735e as /var/lib/containers/storage/overlay/8872e0cb5314b16ee0111ed12766e11e60dd706010199a1dbc0f2046bf1eb964/merged INFO: umounting image eee3feca625505a534e2f5b3e36aae2f6c3e3e929f8b5a4701e335a06a83735e (/var/lib/containers/storage/overlay/8872e0cb5314b16ee0111ed12766e11e60dd706010199a1dbc0f2046bf1eb964/merged) with podman image umount INFO: Removing image mock-bootstrap-a073855e-7605-4239-a88f-1b000e61a1b1 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-x86_64-1769501915.991329/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.x86_64 rpm-sequoia-1.9.0.3-1.el10.x86_64 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 11 kB/s | 2.4 kB 00:00 CentOS Stream 10 - BaseOS 9.6 MB/s | 6.9 MB 00:00 CentOS Stream 10 - AppStream 2.0 MB/s | 3.5 MB 00:01 CentOS Stream 10 - CRB 2.7 MB/s | 795 kB 00:00 CentOS Stream 10 - Extras packages 9.3 kB/s | 8.3 kB 00:00 Extra Packages for Enterprise Linux 10 - x86_64 22 MB/s | 6.2 MB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: bash x86_64 5.2.26-6.el10 baseos 1.8 M bzip2 x86_64 1.0.8-25.el10 baseos 54 k centos-stream-release noarch 10.0-19.el10 baseos 30 k coreutils x86_64 9.5-6.el10 baseos 1.1 M cpio x86_64 2.15-3.el10 baseos 292 k diffutils x86_64 3.10-8.el10 baseos 409 k epel-rpm-macros noarch 10-6.el10_2 epel 8.2 k findutils x86_64 1:4.10.0-5.el10 baseos 551 k gawk x86_64 5.3.0-6.el10 baseos 1.1 M glibc-minimal-langpack x86_64 2.39-99.el10 baseos 39 k grep x86_64 3.11-10.el10 baseos 301 k gzip x86_64 1.13-3.el10 baseos 170 k info x86_64 7.1-6.el10 baseos 183 k patch x86_64 2.7.6-26.el10 appstream 132 k redhat-rpm-config noarch 295-1.el10 appstream 74 k rpm-build x86_64 4.19.1.1-21.el10 appstream 75 k sed x86_64 4.9-3.el10 baseos 318 k shadow-utils x86_64 2:4.15.0-9.el10 baseos 1.3 M tar x86_64 2:1.35-10.el10 baseos 864 k unzip x86_64 6.0-69.el10 baseos 190 k util-linux x86_64 2.40.2-13.el10 baseos 1.3 M which x86_64 2.21-44.el10 baseos 42 k xz x86_64 1:5.6.2-4.el10 baseos 481 k Installing dependencies: alternatives x86_64 1.30-2.el10 baseos 42 k ansible-srpm-macros noarch 1-16.1.el10_0 epel 20 k audit-libs x86_64 4.0.3-5.el10 baseos 131 k authselect x86_64 1.5.0-8.el10 baseos 144 k authselect-libs x86_64 1.5.0-8.el10 baseos 223 k basesystem noarch 11-22.el10 baseos 4.3 k binutils x86_64 2.41-60.el10 baseos 6.4 M binutils-gold x86_64 2.41-60.el10 baseos 797 k bzip2-libs x86_64 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 x86_64 9.5-6.el10 baseos 2.1 M cracklib x86_64 2.9.11-8.el10 baseos 96 k cracklib-dicts x86_64 2.9.11-8.el10 baseos 3.6 M crypto-policies noarch 20251127-1.git27c2902.el10 baseos 98 k curl x86_64 8.12.1-4.el10 baseos 217 k cyrus-sasl-lib x86_64 2.1.28-27.el10 baseos 106 k debugedit x86_64 5.1-8.el10 appstream 80 k dwz x86_64 0.16-1.el10 appstream 140 k ed x86_64 1.20-5.el10 baseos 83 k efi-srpm-macros noarch 6-6.el10 appstream 24 k elfutils x86_64 0.194-1.el10 baseos 573 k elfutils-debuginfod-client x86_64 0.194-1.el10 baseos 43 k elfutils-default-yama-scope noarch 0.194-1.el10 baseos 8.3 k elfutils-libelf x86_64 0.194-1.el10 baseos 201 k elfutils-libs x86_64 0.194-1.el10 baseos 267 k file x86_64 5.45-8.el10 baseos 49 k file-libs x86_64 5.45-8.el10 baseos 764 k filesystem x86_64 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 x86_64 16.3-2.el10 appstream 4.4 M gdbm x86_64 1:1.23-14.el10 baseos 151 k gdbm-libs x86_64 1:1.23-14.el10 baseos 57 k ghc-srpm-macros noarch 1.9.2-1.el10_0 epel 9.1 k glibc x86_64 2.39-99.el10 baseos 2.1 M glibc-common x86_64 2.39-99.el10 baseos 333 k glibc-gconv-extra x86_64 2.39-99.el10 baseos 1.7 M gmp x86_64 1:6.2.1-12.el10 baseos 318 k go-srpm-macros noarch 3.8.0-1.el10 appstream 27 k jansson x86_64 2.14-3.el10 baseos 46 k json-c x86_64 0.18-3.el10 baseos 45 k kernel-srpm-macros noarch 1.0-27.el10 appstream 8.7 k keyutils-libs x86_64 1.6.3-5.el10 baseos 33 k krb5-libs x86_64 1.21.3-8.el10 baseos 767 k libacl x86_64 2.3.2-4.el10 baseos 25 k libarchive x86_64 3.7.7-4.el10 baseos 414 k libattr x86_64 2.5.2-5.el10 baseos 19 k libblkid x86_64 2.40.2-13.el10 baseos 124 k libbrotli x86_64 1.1.0-7.el10 baseos 344 k libcap x86_64 2.69-7.el10 baseos 91 k libcap-ng x86_64 0.8.4-6.el10 baseos 33 k libcom_err x86_64 1.47.1-5.el10 baseos 26 k libcurl x86_64 8.12.1-4.el10 baseos 368 k libeconf x86_64 0.6.2-4.el10 baseos 33 k libevent x86_64 2.1.12-16.el10 baseos 261 k libfdisk x86_64 2.40.2-13.el10 baseos 159 k libffi x86_64 3.4.4-10.el10 baseos 41 k libgcc x86_64 14.3.1-4.2.el10 baseos 147 k libgomp x86_64 14.3.1-4.2.el10 baseos 370 k libidn2 x86_64 2.3.7-3.el10 baseos 118 k libmount x86_64 2.40.2-13.el10 baseos 155 k libnghttp2 x86_64 1.64.0-2.el10 baseos 78 k libpkgconf x86_64 2.1.0-3.el10 baseos 39 k libpsl x86_64 0.21.5-6.el10 baseos 65 k libpwquality x86_64 1.4.5-12.el10 baseos 123 k libselinux x86_64 3.9-3.el10 baseos 97 k libsemanage x86_64 3.9-2.el10 baseos 121 k libsepol x86_64 3.9-1.el10 baseos 348 k libsmartcols x86_64 2.40.2-13.el10 baseos 83 k libssh x86_64 0.11.1-3.el10 baseos 233 k libssh-config noarch 0.11.1-3.el10 baseos 8.4 k libstdc++ x86_64 14.3.1-4.2.el10 baseos 926 k libtasn1 x86_64 4.20.0-1.el10 baseos 75 k libunistring x86_64 1.1-10.el10 baseos 548 k libutempter x86_64 1.2.1-15.el10 baseos 27 k libuuid x86_64 2.40.2-13.el10 baseos 28 k libverto x86_64 0.3.2-10.el10 baseos 22 k libxcrypt x86_64 4.4.36-10.el10 baseos 120 k libxml2 x86_64 2.12.5-9.el10 baseos 692 k libzstd x86_64 1.5.5-9.el10 baseos 292 k lua-libs x86_64 5.4.6-7.el10 baseos 132 k lua-srpm-macros noarch 1-15.el10 appstream 9.8 k lz4-libs x86_64 1.9.4-8.el10 baseos 68 k mpfr x86_64 4.2.1-6.el10 baseos 346 k ncurses-base noarch 6.4-14.20240127.el10 baseos 100 k ncurses-libs x86_64 6.4-14.20240127.el10 baseos 338 k ocaml-srpm-macros noarch 10-4.el10 appstream 10 k openblas-srpm-macros noarch 2-19.el10 appstream 8.7 k openldap x86_64 2.6.10-1.el10 baseos 239 k openssl-fips-provider x86_64 1:3.5.1-6.el10 baseos 812 k openssl-libs x86_64 1:3.5.1-6.el10 baseos 2.3 M p11-kit x86_64 0.26.1-1.el10 baseos 559 k p11-kit-trust x86_64 0.26.1-1.el10 baseos 141 k package-notes-srpm-macros noarch 0.5-13.el10 appstream 10 k pam x86_64 1.6.1-9.el10 baseos 584 k pam-libs x86_64 1.6.1-9.el10 baseos 56 k pcre2 x86_64 10.44-1.el10.3 baseos 248 k pcre2-syntax noarch 10.44-1.el10.3 baseos 151 k perl-srpm-macros noarch 1-57.el10 appstream 9.5 k pkgconf x86_64 2.1.0-3.el10 baseos 45 k pkgconf-m4 noarch 2.1.0-3.el10 baseos 15 k pkgconf-pkg-config x86_64 2.1.0-3.el10 baseos 11 k popt x86_64 1.19-8.el10 baseos 66 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 x86_64 8.2-11.el10 baseos 214 k rpm x86_64 4.19.1.1-21.el10 baseos 560 k rpm-build-libs x86_64 4.19.1.1-21.el10 baseos 92 k rpm-libs x86_64 4.19.1.1-21.el10 baseos 309 k rpm-sequoia x86_64 1.9.0.3-1.el10 baseos 975 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 x86_64 3.46.1-5.el10 baseos 745 k systemd-libs x86_64 257-21.el10 baseos 828 k util-linux-core x86_64 2.40.2-13.el10 baseos 550 k xz-libs x86_64 1:5.6.2-4.el10 baseos 113 k zip x86_64 3.0-45.el10 baseos 270 k zlib-ng-compat x86_64 2.2.3-3.el10 baseos 76 k zstd x86_64 1.5.5-9.el10 baseos 464 k Transaction Summary ================================================================================ Install 147 Packages Total download size: 61 M Installed size: 188 M Downloading Packages: (1/147): alternatives-1.30-2.el10.x86_64.rpm 1.3 MB/s | 42 kB 00:00 (2/147): authselect-1.5.0-8.el10.x86_64.rpm 4.1 MB/s | 144 kB 00:00 (3/147): audit-libs-4.0.3-5.el10.x86_64.rpm 3.6 MB/s | 131 kB 00:00 (4/147): basesystem-11-22.el10.noarch.rpm 658 kB/s | 4.3 kB 00:00 (5/147): authselect-libs-1.5.0-8.el10.x86_64.rp 7.4 MB/s | 223 kB 00:00 (6/147): binutils-gold-2.41-60.el10.x86_64.rpm 21 MB/s | 797 kB 00:00 (7/147): bzip2-1.0.8-25.el10.x86_64.rpm 6.9 MB/s | 54 kB 00:00 (8/147): bzip2-libs-1.0.8-25.el10.x86_64.rpm 5.4 MB/s | 42 kB 00:00 (9/147): bash-5.2.26-6.el10.x86_64.rpm 22 MB/s | 1.8 MB 00:00 (10/147): centos-gpg-keys-10.0-19.el10.noarch.r 3.7 MB/s | 26 kB 00:00 (11/147): ca-certificates-2025.2.80_v9.0.305-10 69 MB/s | 1.1 MB 00:00 (12/147): centos-stream-release-10.0-19.el10.no 4.0 MB/s | 30 kB 00:00 (13/147): centos-stream-repos-10.0-19.el10.noar 1.5 MB/s | 12 kB 00:00 (14/147): coreutils-9.5-6.el10.x86_64.rpm 79 MB/s | 1.1 MB 00:00 (15/147): coreutils-common-9.5-6.el10.x86_64.rp 124 MB/s | 2.1 MB 00:00 (16/147): cpio-2.15-3.el10.x86_64.rpm 37 MB/s | 292 kB 00:00 (17/147): binutils-2.41-60.el10.x86_64.rpm 53 MB/s | 6.4 MB 00:00 (18/147): cracklib-2.9.11-8.el10.x86_64.rpm 12 MB/s | 96 kB 00:00 (19/147): curl-8.12.1-4.el10.x86_64.rpm 31 MB/s | 217 kB 00:00 (20/147): crypto-policies-20251127-1.git27c2902 12 MB/s | 98 kB 00:00 (21/147): cracklib-dicts-2.9.11-8.el10.x86_64.r 196 MB/s | 3.6 MB 00:00 (22/147): cyrus-sasl-lib-2.1.28-27.el10.x86_64. 14 MB/s | 106 kB 00:00 (23/147): diffutils-3.10-8.el10.x86_64.rpm 53 MB/s | 409 kB 00:00 (24/147): ed-1.20-5.el10.x86_64.rpm 11 MB/s | 83 kB 00:00 (25/147): elfutils-debuginfod-client-0.194-1.el 6.3 MB/s | 43 kB 00:00 (26/147): elfutils-0.194-1.el10.x86_64.rpm 67 MB/s | 573 kB 00:00 (27/147): elfutils-default-yama-scope-0.194-1.e 1.2 MB/s | 8.3 kB 00:00 (28/147): elfutils-libelf-0.194-1.el10.x86_64.r 27 MB/s | 201 kB 00:00 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jansson-2.14-3.el10.x86_64.rpm 6.6 MB/s | 46 kB 00:00 (45/147): info-7.1-6.el10.x86_64.rpm 22 MB/s | 183 kB 00:00 (46/147): json-c-0.18-3.el10.x86_64.rpm 6.3 MB/s | 45 kB 00:00 (47/147): keyutils-libs-1.6.3-5.el10.x86_64.rpm 4.3 MB/s | 33 kB 00:00 (48/147): krb5-libs-1.21.3-8.el10.x86_64.rpm 93 MB/s | 767 kB 00:00 (49/147): libacl-2.3.2-4.el10.x86_64.rpm 3.6 MB/s | 25 kB 00:00 (50/147): libattr-2.5.2-5.el10.x86_64.rpm 2.8 MB/s | 19 kB 00:00 (51/147): libarchive-3.7.7-4.el10.x86_64.rpm 49 MB/s | 414 kB 00:00 (52/147): libblkid-2.40.2-13.el10.x86_64.rpm 17 MB/s | 124 kB 00:00 (53/147): libbrotli-1.1.0-7.el10.x86_64.rpm 47 MB/s | 344 kB 00:00 (54/147): libcap-2.69-7.el10.x86_64.rpm 12 MB/s | 91 kB 00:00 (55/147): libcap-ng-0.8.4-6.el10.x86_64.rpm 4.7 MB/s | 33 kB 00:00 (56/147): libcom_err-1.47.1-5.el10.x86_64.rpm 3.8 MB/s | 26 kB 00:00 (57/147): libeconf-0.6.2-4.el10.x86_64.rpm 4.5 MB/s | 33 kB 00:00 (58/147): libcurl-8.12.1-4.el10.x86_64.rpm 43 MB/s | 368 kB 00:00 (59/147): 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kB 00:00 (147/147): gdb-minimal-16.3-2.el10.x86_64.rpm 1.3 MB/s | 4.4 MB 00:03 -------------------------------------------------------------------------------- Total 13 MB/s | 61 MB 00:04 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 - x86_64 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.x86_64 1/1 Preparing : 1/1 Installing : libgcc-14.3.1-4.2.el10.x86_64 1/147 Running scriptlet: libgcc-14.3.1-4.2.el10.x86_64 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 : ncurses-base-6.4-14.20240127.el10.noarch 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p11-kit-trust-0.26.1-1.el10.x86_64 83/147 Running scriptlet: p11-kit-trust-0.26.1-1.el10.x86_64 83/147 Installing : openssl-fips-provider-1:3.5.1-6.el10.x86_64 84/147 Installing : openssl-libs-1:3.5.1-6.el10.x86_64 85/147 Installing : coreutils-9.5-6.el10.x86_64 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.x86_64 88/147 Installing : gzip-1.13-3.el10.x86_64 89/147 Installing : cracklib-2.9.11-8.el10.x86_64 90/147 Installing : cracklib-dicts-2.9.11-8.el10.x86_64 91/147 Installing : libpwquality-1.4.5-12.el10.x86_64 92/147 Installing : libevent-2.1.12-16.el10.x86_64 93/147 Installing : rpm-sequoia-1.9.0.3-1.el10.x86_64 94/147 Installing : zip-3.0-45.el10.x86_64 95/147 Installing : cyrus-sasl-lib-2.1.28-27.el10.x86_64 96/147 Installing : openldap-2.6.10-1.el10.x86_64 97/147 Installing : gdbm-1:1.23-14.el10.x86_64 98/147 Installing : pam-1.6.1-9.el10.x86_64 99/147 Installing : libfdisk-2.40.2-13.el10.x86_64 100/147 Installing : libxml2-2.12.5-9.el10.x86_64 101/147 Installing : libarchive-3.7.7-4.el10.x86_64 102/147 Installing : bzip2-1.0.8-25.el10.x86_64 103/147 Installing : sqlite-libs-3.46.1-5.el10.x86_64 104/147 Installing : rpm-libs-4.19.1.1-21.el10.x86_64 105/147 Installing : ed-1.20-5.el10.x86_64 106/147 Installing : patch-2.7.6-26.el10.x86_64 107/147 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.x86_64 109/147 Installing : diffutils-3.10-8.el10.x86_64 110/147 Installing : json-c-0.18-3.el10.x86_64 111/147 Installing : keyutils-libs-1.6.3-5.el10.x86_64 112/147 Installing : libbrotli-1.1.0-7.el10.x86_64 113/147 Installing : libcom_err-1.47.1-5.el10.x86_64 114/147 Installing : libgomp-14.3.1-4.2.el10.x86_64 115/147 Installing : libnghttp2-1.64.0-2.el10.x86_64 116/147 Installing : libpkgconf-2.1.0-3.el10.x86_64 117/147 Installing : pkgconf-2.1.0-3.el10.x86_64 118/147 Installing : pkgconf-pkg-config-2.1.0-3.el10.x86_64 119/147 Installing : libverto-0.3.2-10.el10.x86_64 120/147 Installing : krb5-libs-1.21.3-8.el10.x86_64 121/147 Installing : libssh-0.11.1-3.el10.x86_64 122/147 Installing : libcurl-8.12.1-4.el10.x86_64 123/147 Installing : elfutils-libs-0.194-1.el10.x86_64 124/147 Installing : elfutils-debuginfod-client-0.194-1.el10.x86_64 125/147 Installing : binutils-gold-2.41-60.el10.x86_64 126/147 Running scriptlet: binutils-gold-2.41-60.el10.x86_64 126/147 Installing : binutils-2.41-60.el10.x86_64 127/147 Running scriptlet: binutils-2.41-60.el10.x86_64 127/147 Installing : elfutils-0.194-1.el10.x86_64 128/147 Installing : gdb-minimal-16.3-2.el10.x86_64 129/147 Installing : debugedit-5.1-8.el10.x86_64 130/147 Installing : rpm-build-libs-4.19.1.1-21.el10.x86_64 131/147 Installing : curl-8.12.1-4.el10.x86_64 132/147 Running scriptlet: rpm-4.19.1.1-21.el10.x86_64 133/147 Installing : rpm-4.19.1.1-21.el10.x86_64 133/147 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.x86_64 141/147 Installing : pyproject-srpm-macros-1.18.5-1.el10.noarch 142/147 Installing : util-linux-2.40.2-13.el10.x86_64 143/147 Running scriptlet: util-linux-2.40.2-13.el10.x86_64 143/147 Installing : authselect-1.5.0-8.el10.x86_64 144/147 Installing : which-2.21-44.el10.x86_64 145/147 Installing : info-7.1-6.el10.x86_64 146/147 Installing : epel-rpm-macros-10-6.el10_2.noarch 147/147 Running scriptlet: filesystem-3.18-17.el10.x86_64 147/147 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar 147/147 Running scriptlet: authselect-libs-1.5.0-8.el10.x86_64 147/147 Running scriptlet: rpm-4.19.1.1-21.el10.x86_64 147/147 Running scriptlet: epel-rpm-macros-10-6.el10_2.noarch 147/147 Installed: alternatives-1.30-2.el10.x86_64 ansible-srpm-macros-1-16.1.el10_0.noarch audit-libs-4.0.3-5.el10.x86_64 authselect-1.5.0-8.el10.x86_64 authselect-libs-1.5.0-8.el10.x86_64 basesystem-11-22.el10.noarch bash-5.2.26-6.el10.x86_64 binutils-2.41-60.el10.x86_64 binutils-gold-2.41-60.el10.x86_64 bzip2-1.0.8-25.el10.x86_64 bzip2-libs-1.0.8-25.el10.x86_64 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.x86_64 coreutils-common-9.5-6.el10.x86_64 cpio-2.15-3.el10.x86_64 cracklib-2.9.11-8.el10.x86_64 cracklib-dicts-2.9.11-8.el10.x86_64 crypto-policies-20251127-1.git27c2902.el10.noarch curl-8.12.1-4.el10.x86_64 cyrus-sasl-lib-2.1.28-27.el10.x86_64 debugedit-5.1-8.el10.x86_64 diffutils-3.10-8.el10.x86_64 dwz-0.16-1.el10.x86_64 ed-1.20-5.el10.x86_64 efi-srpm-macros-6-6.el10.noarch elfutils-0.194-1.el10.x86_64 elfutils-debuginfod-client-0.194-1.el10.x86_64 elfutils-default-yama-scope-0.194-1.el10.noarch elfutils-libelf-0.194-1.el10.x86_64 elfutils-libs-0.194-1.el10.x86_64 epel-rpm-macros-10-6.el10_2.noarch file-5.45-8.el10.x86_64 file-libs-5.45-8.el10.x86_64 filesystem-3.18-17.el10.x86_64 findutils-1:4.10.0-5.el10.x86_64 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.x86_64 gdb-minimal-16.3-2.el10.x86_64 gdbm-1:1.23-14.el10.x86_64 gdbm-libs-1:1.23-14.el10.x86_64 ghc-srpm-macros-1.9.2-1.el10_0.noarch glibc-2.39-99.el10.x86_64 glibc-common-2.39-99.el10.x86_64 glibc-gconv-extra-2.39-99.el10.x86_64 glibc-minimal-langpack-2.39-99.el10.x86_64 gmp-1:6.2.1-12.el10.x86_64 go-srpm-macros-3.8.0-1.el10.noarch grep-3.11-10.el10.x86_64 gzip-1.13-3.el10.x86_64 info-7.1-6.el10.x86_64 jansson-2.14-3.el10.x86_64 json-c-0.18-3.el10.x86_64 kernel-srpm-macros-1.0-27.el10.noarch keyutils-libs-1.6.3-5.el10.x86_64 krb5-libs-1.21.3-8.el10.x86_64 libacl-2.3.2-4.el10.x86_64 libarchive-3.7.7-4.el10.x86_64 libattr-2.5.2-5.el10.x86_64 libblkid-2.40.2-13.el10.x86_64 libbrotli-1.1.0-7.el10.x86_64 libcap-2.69-7.el10.x86_64 libcap-ng-0.8.4-6.el10.x86_64 libcom_err-1.47.1-5.el10.x86_64 libcurl-8.12.1-4.el10.x86_64 libeconf-0.6.2-4.el10.x86_64 libevent-2.1.12-16.el10.x86_64 libfdisk-2.40.2-13.el10.x86_64 libffi-3.4.4-10.el10.x86_64 libgcc-14.3.1-4.2.el10.x86_64 libgomp-14.3.1-4.2.el10.x86_64 libidn2-2.3.7-3.el10.x86_64 libmount-2.40.2-13.el10.x86_64 libnghttp2-1.64.0-2.el10.x86_64 libpkgconf-2.1.0-3.el10.x86_64 libpsl-0.21.5-6.el10.x86_64 libpwquality-1.4.5-12.el10.x86_64 libselinux-3.9-3.el10.x86_64 libsemanage-3.9-2.el10.x86_64 libsepol-3.9-1.el10.x86_64 libsmartcols-2.40.2-13.el10.x86_64 libssh-0.11.1-3.el10.x86_64 libssh-config-0.11.1-3.el10.noarch libstdc++-14.3.1-4.2.el10.x86_64 libtasn1-4.20.0-1.el10.x86_64 libunistring-1.1-10.el10.x86_64 libutempter-1.2.1-15.el10.x86_64 libuuid-2.40.2-13.el10.x86_64 libverto-0.3.2-10.el10.x86_64 libxcrypt-4.4.36-10.el10.x86_64 libxml2-2.12.5-9.el10.x86_64 libzstd-1.5.5-9.el10.x86_64 lua-libs-5.4.6-7.el10.x86_64 lua-srpm-macros-1-15.el10.noarch lz4-libs-1.9.4-8.el10.x86_64 mpfr-4.2.1-6.el10.x86_64 ncurses-base-6.4-14.20240127.el10.noarch ncurses-libs-6.4-14.20240127.el10.x86_64 ocaml-srpm-macros-10-4.el10.noarch openblas-srpm-macros-2-19.el10.noarch openldap-2.6.10-1.el10.x86_64 openssl-fips-provider-1:3.5.1-6.el10.x86_64 openssl-libs-1:3.5.1-6.el10.x86_64 p11-kit-0.26.1-1.el10.x86_64 p11-kit-trust-0.26.1-1.el10.x86_64 package-notes-srpm-macros-0.5-13.el10.noarch pam-1.6.1-9.el10.x86_64 pam-libs-1.6.1-9.el10.x86_64 patch-2.7.6-26.el10.x86_64 pcre2-10.44-1.el10.3.x86_64 pcre2-syntax-10.44-1.el10.3.noarch perl-srpm-macros-1-57.el10.noarch pkgconf-2.1.0-3.el10.x86_64 pkgconf-m4-2.1.0-3.el10.noarch pkgconf-pkg-config-2.1.0-3.el10.x86_64 popt-1.19-8.el10.x86_64 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.x86_64 redhat-rpm-config-295-1.el10.noarch rpm-4.19.1.1-21.el10.x86_64 rpm-build-4.19.1.1-21.el10.x86_64 rpm-build-libs-4.19.1.1-21.el10.x86_64 rpm-libs-4.19.1.1-21.el10.x86_64 rpm-sequoia-1.9.0.3-1.el10.x86_64 rust-toolset-srpm-macros-1.92.0-1.el10.noarch sed-4.9-3.el10.x86_64 setup-2.14.5-7.el10.noarch shadow-utils-2:4.15.0-9.el10.x86_64 sqlite-libs-3.46.1-5.el10.x86_64 systemd-libs-257-21.el10.x86_64 tar-2:1.35-10.el10.x86_64 unzip-6.0-69.el10.x86_64 util-linux-2.40.2-13.el10.x86_64 util-linux-core-2.40.2-13.el10.x86_64 which-2.21-44.el10.x86_64 xz-1:5.6.2-4.el10.x86_64 xz-libs-1:5.6.2-4.el10.x86_64 zip-3.0-45.el10.x86_64 zlib-ng-compat-2.2.3-3.el10.x86_64 zstd-1.5.5-9.el10.x86_64 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.x86_64 ansible-srpm-macros-1-16.1.el10_0.noarch audit-libs-4.0.3-5.el10.x86_64 authselect-1.5.0-8.el10.x86_64 authselect-libs-1.5.0-8.el10.x86_64 basesystem-11-22.el10.noarch bash-5.2.26-6.el10.x86_64 binutils-2.41-60.el10.x86_64 binutils-gold-2.41-60.el10.x86_64 bzip2-1.0.8-25.el10.x86_64 bzip2-libs-1.0.8-25.el10.x86_64 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.x86_64 coreutils-common-9.5-6.el10.x86_64 cpio-2.15-3.el10.x86_64 cracklib-2.9.11-8.el10.x86_64 cracklib-dicts-2.9.11-8.el10.x86_64 crypto-policies-20251127-1.git27c2902.el10.noarch curl-8.12.1-4.el10.x86_64 cyrus-sasl-lib-2.1.28-27.el10.x86_64 debugedit-5.1-8.el10.x86_64 diffutils-3.10-8.el10.x86_64 dwz-0.16-1.el10.x86_64 ed-1.20-5.el10.x86_64 efi-srpm-macros-6-6.el10.noarch elfutils-0.194-1.el10.x86_64 elfutils-debuginfod-client-0.194-1.el10.x86_64 elfutils-default-yama-scope-0.194-1.el10.noarch elfutils-libelf-0.194-1.el10.x86_64 elfutils-libs-0.194-1.el10.x86_64 epel-rpm-macros-10-6.el10_2.noarch file-5.45-8.el10.x86_64 file-libs-5.45-8.el10.x86_64 filesystem-3.18-17.el10.x86_64 findutils-4.10.0-5.el10.x86_64 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.x86_64 gdb-minimal-16.3-2.el10.x86_64 gdbm-1.23-14.el10.x86_64 gdbm-libs-1.23-14.el10.x86_64 ghc-srpm-macros-1.9.2-1.el10_0.noarch glibc-2.39-99.el10.x86_64 glibc-common-2.39-99.el10.x86_64 glibc-gconv-extra-2.39-99.el10.x86_64 glibc-minimal-langpack-2.39-99.el10.x86_64 gmp-6.2.1-12.el10.x86_64 go-srpm-macros-3.8.0-1.el10.noarch gpg-pubkey-8483c65d-5ccc5b19 gpg-pubkey-e37ed158-65785fa9 grep-3.11-10.el10.x86_64 gzip-1.13-3.el10.x86_64 info-7.1-6.el10.x86_64 jansson-2.14-3.el10.x86_64 json-c-0.18-3.el10.x86_64 kernel-srpm-macros-1.0-27.el10.noarch keyutils-libs-1.6.3-5.el10.x86_64 krb5-libs-1.21.3-8.el10.x86_64 libacl-2.3.2-4.el10.x86_64 libarchive-3.7.7-4.el10.x86_64 libattr-2.5.2-5.el10.x86_64 libblkid-2.40.2-13.el10.x86_64 libbrotli-1.1.0-7.el10.x86_64 libcap-2.69-7.el10.x86_64 libcap-ng-0.8.4-6.el10.x86_64 libcom_err-1.47.1-5.el10.x86_64 libcurl-8.12.1-4.el10.x86_64 libeconf-0.6.2-4.el10.x86_64 libevent-2.1.12-16.el10.x86_64 libfdisk-2.40.2-13.el10.x86_64 libffi-3.4.4-10.el10.x86_64 libgcc-14.3.1-4.2.el10.x86_64 libgomp-14.3.1-4.2.el10.x86_64 libidn2-2.3.7-3.el10.x86_64 libmount-2.40.2-13.el10.x86_64 libnghttp2-1.64.0-2.el10.x86_64 libpkgconf-2.1.0-3.el10.x86_64 libpsl-0.21.5-6.el10.x86_64 libpwquality-1.4.5-12.el10.x86_64 libselinux-3.9-3.el10.x86_64 libsemanage-3.9-2.el10.x86_64 libsepol-3.9-1.el10.x86_64 libsmartcols-2.40.2-13.el10.x86_64 libssh-0.11.1-3.el10.x86_64 libssh-config-0.11.1-3.el10.noarch libstdc++-14.3.1-4.2.el10.x86_64 libtasn1-4.20.0-1.el10.x86_64 libunistring-1.1-10.el10.x86_64 libutempter-1.2.1-15.el10.x86_64 libuuid-2.40.2-13.el10.x86_64 libverto-0.3.2-10.el10.x86_64 libxcrypt-4.4.36-10.el10.x86_64 libxml2-2.12.5-9.el10.x86_64 libzstd-1.5.5-9.el10.x86_64 lua-libs-5.4.6-7.el10.x86_64 lua-srpm-macros-1-15.el10.noarch lz4-libs-1.9.4-8.el10.x86_64 mpfr-4.2.1-6.el10.x86_64 ncurses-base-6.4-14.20240127.el10.noarch ncurses-libs-6.4-14.20240127.el10.x86_64 ocaml-srpm-macros-10-4.el10.noarch openblas-srpm-macros-2-19.el10.noarch openldap-2.6.10-1.el10.x86_64 openssl-fips-provider-3.5.1-6.el10.x86_64 openssl-libs-3.5.1-6.el10.x86_64 p11-kit-0.26.1-1.el10.x86_64 p11-kit-trust-0.26.1-1.el10.x86_64 package-notes-srpm-macros-0.5-13.el10.noarch pam-1.6.1-9.el10.x86_64 pam-libs-1.6.1-9.el10.x86_64 patch-2.7.6-26.el10.x86_64 pcre2-10.44-1.el10.3.x86_64 pcre2-syntax-10.44-1.el10.3.noarch perl-srpm-macros-1-57.el10.noarch pkgconf-2.1.0-3.el10.x86_64 pkgconf-m4-2.1.0-3.el10.noarch pkgconf-pkg-config-2.1.0-3.el10.x86_64 popt-1.19-8.el10.x86_64 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.x86_64 redhat-rpm-config-295-1.el10.noarch rpm-4.19.1.1-21.el10.x86_64 rpm-build-4.19.1.1-21.el10.x86_64 rpm-build-libs-4.19.1.1-21.el10.x86_64 rpm-libs-4.19.1.1-21.el10.x86_64 rpm-sequoia-1.9.0.3-1.el10.x86_64 rust-toolset-srpm-macros-1.92.0-1.el10.noarch sed-4.9-3.el10.x86_64 setup-2.14.5-7.el10.noarch shadow-utils-4.15.0-9.el10.x86_64 sqlite-libs-3.46.1-5.el10.x86_64 systemd-libs-257-21.el10.x86_64 tar-1.35-10.el10.x86_64 unzip-6.0-69.el10.x86_64 util-linux-2.40.2-13.el10.x86_64 util-linux-core-2.40.2-13.el10.x86_64 which-2.21-44.el10.x86_64 xz-5.6.2-4.el10.x86_64 xz-libs-5.6.2-4.el10.x86_64 zip-3.0-45.el10.x86_64 zlib-ng-compat-2.2.3-3.el10.x86_64 zstd-1.5.5-9.el10.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 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-x86_64-1769501915.991329/root/var/log/dnf.rpm.log /var/lib/mock/centos-stream+epel-10-x86_64-1769501915.991329/root/var/log/dnf.librepo.log /var/lib/mock/centos-stream+epel-10-x86_64-1769501915.991329/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-05b8sndb/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-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-x86_64-bootstrap-1769501915.991329/root. INFO: reusing tmpfs at /var/lib/mock/centos-stream+epel-10-x86_64-bootstrap-1769501915.991329/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-x86_64-1769501915.991329/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.x86_64 rpm-sequoia-1.9.0.3-1.el10.x86_64 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: x86_64 Building for target x86_64 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 29 kB/s | 1.5 kB 00:00 CentOS Stream 10 - BaseOS 53 kB/s | 4.5 kB 00:00 CentOS Stream 10 - AppStream 30 kB/s | 5.5 kB 00:00 CentOS Stream 10 - CRB 95 kB/s | 4.4 kB 00:00 CentOS Stream 10 - Extras packages 41 kB/s | 7.3 kB 00:00 Extra Packages for Enterprise Linux 10 - x86_64 307 kB/s | 34 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: gcc x86_64 14.3.1-4.2.el10 appstream 38 M htslib-devel x86_64 1.23-1.el10 copr_base 107 k htslib-tools x86_64 1.23-1.el10 copr_base 754 k make x86_64 1:4.4.1-9.el10 baseos 587 k ncurses-devel x86_64 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 x86_64 4:5.40.2-514.el10 appstream 73 k perl-lib x86_64 0.65-514.el10 appstream 16 k zlib-ng-compat-devel x86_64 2.2.3-3.el10 appstream 36 k Installing dependencies: annobin-docs noarch 13.02-2.el10 appstream 87 k annobin-plugin-gcc x86_64 13.02-2.el10 appstream 997 k cmake-filesystem x86_64 3.31.8-1.el10 appstream 21 k cpp x86_64 14.3.1-4.2.el10 appstream 13 M gcc-plugin-annobin x86_64 14.3.1-4.2.el10 appstream 69 k glibc-devel x86_64 2.39-99.el10 appstream 598 k groff-base x86_64 1.23.0-10.el10 baseos 1.1 M htslib x86_64 1.23-1.el10 copr_base 593 k kernel-headers x86_64 6.12.0-191.el10 appstream 3.1 M libmpc x86_64 1.3.1-7.el10 appstream 71 k libxcrypt-devel x86_64 4.4.36-10.el10 appstream 30 k ncurses x86_64 6.4-14.20240127.el10 baseos 423 k ncurses-c++-libs x86_64 6.4-14.20240127.el10 appstream 39 k perl-AutoLoader noarch 5.74-514.el10 appstream 22 k perl-B x86_64 1.89-514.el10 appstream 178 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 x86_64 2.189-512.el10 baseos 57 k perl-Digest noarch 1.20-511.el10 baseos 26 k perl-Digest-MD5 x86_64 2.59-6.el10 baseos 37 k perl-DynaLoader x86_64 1.56-514.el10 appstream 27 k perl-Encode x86_64 4:3.21-511.el10 baseos 1.1 M perl-Errno x86_64 1.38-514.el10 appstream 16 k perl-Exporter noarch 5.78-511.el10 baseos 32 k perl-Fcntl x86_64 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 x86_64 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 x86_64 3.16-511.el10 baseos 31 k perl-Mozilla-CA noarch 20231213-5.el10 baseos 15 k perl-Net-SSLeay x86_64 1.94-8.el10 appstream 380 k perl-POSIX x86_64 2.20-514.el10 appstream 97 k perl-PathTools x86_64 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 x86_64 5:1.63-511.el10 baseos 74 k perl-SelectSaver noarch 1.02-514.el10 appstream 12 k perl-Socket x86_64 4:2.038-511.el10 baseos 56 k perl-Storable x86_64 1:3.32-511.el10 baseos 99 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 x86_64 4:5.40.2-514.el10 appstream 2.4 M perl-locale noarch 1.12-514.el10 appstream 14 k perl-mro x86_64 1.29-514.el10 appstream 31 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 78 Packages Total download size: 67 M Installed size: 193 M Downloading Packages: (1/78): htslib-devel-1.23-1.el10.x86_64.rpm 973 kB/s | 107 kB 00:00 (2/78): htslib-tools-1.23-1.el10.x86_64.rpm 3.9 MB/s | 754 kB 00:00 (3/78): htslib-1.23-1.el10.x86_64.rpm 3.0 MB/s | 593 kB 00:00 (4/78): ncurses-6.4-14.20240127.el10.x86_64.rpm 2.9 MB/s | 423 kB 00:00 (5/78): perl-Carp-1.54-511.el10.noarch.rpm 1.6 MB/s | 30 kB 00:00 (6/78): perl-Data-Dumper-2.189-512.el10.x86_64. 3.1 MB/s | 57 kB 00:00 (7/78): make-4.4.1-9.el10.x86_64.rpm 2.9 MB/s | 587 kB 00:00 (8/78): perl-Digest-1.20-511.el10.noarch.rpm 1.4 MB/s | 26 kB 00:00 (9/78): perl-Digest-MD5-2.59-6.el10.x86_64.rpm 2.0 MB/s | 37 kB 00:00 (10/78): perl-Exporter-5.78-511.el10.noarch.rpm 1.7 MB/s | 32 kB 00:00 (11/78): perl-File-Temp-0.231.100-512.el10.noar 3.2 MB/s | 60 kB 00:00 (12/78): perl-Getopt-Long-2.58-3.el10.noarch.rp 3.4 MB/s | 65 kB 00:00 (13/78): perl-HTTP-Tiny-0.088-512.el10.noarch.r 3.0 MB/s | 57 kB 00:00 (14/78): perl-Encode-3.21-511.el10.x86_64.rpm 9.8 MB/s | 1.1 MB 00:00 (15/78): perl-IO-Socket-IP-0.42-512.el10.noarch 2.3 MB/s | 43 kB 00:00 (16/78): perl-IO-Socket-SSL-2.085-3.el10.noarch 12 MB/s | 227 kB 00:00 (17/78): perl-MIME-Base64-3.16-511.el10.x86_64. 1.6 MB/s | 31 kB 00:00 (18/78): perl-Mozilla-CA-20231213-5.el10.noarch 811 kB/s | 15 kB 00:00 (19/78): perl-PathTools-3.91-512.el10.x86_64.rp 4.5 MB/s | 85 kB 00:00 (20/78): groff-base-1.23.0-10.el10.x86_64.rpm 2.5 MB/s | 1.1 MB 00:00 (21/78): perl-Pod-Escapes-1.07-511.el10.noarch. 1.0 MB/s | 21 kB 00:00 (22/78): perl-Pod-Perldoc-3.28.01-512.el10.noar 4.2 MB/s | 84 kB 00:00 (23/78): perl-Pod-Usage-2.03-511.el10.noarch.rp 2.2 MB/s | 41 kB 00:00 (24/78): perl-Scalar-List-Utils-1.63-511.el10.x 3.9 MB/s | 74 kB 00:00 (25/78): perl-Socket-2.038-511.el10.x86_64.rpm 3.0 MB/s | 56 kB 00:00 (26/78): perl-Storable-3.32-511.el10.x86_64.rpm 5.3 MB/s | 99 kB 00:00 (27/78): perl-Term-ANSIColor-5.01-512.el10.noar 2.6 MB/s | 49 kB 00:00 (28/78): perl-Term-Cap-1.18-511.el10.noarch.rpm 1.2 MB/s | 23 kB 00:00 (29/78): perl-Pod-Simple-3.45-511.el10.noarch.r 3.0 MB/s | 218 kB 00:00 (30/78): perl-Text-ParseWords-3.31-511.el10.noa 950 kB/s | 17 kB 00:00 (31/78): perl-Text-Tabs+Wrap-2024.001-511.el10. 1.2 MB/s | 23 kB 00:00 (32/78): perl-Time-Local-1.350-511.el10.noarch. 1.9 MB/s | 35 kB 00:00 (33/78): perl-constant-1.33-512.el10.noarch.rpm 1.3 MB/s | 24 kB 00:00 (34/78): perl-libnet-3.15-512.el10.noarch.rpm 6.8 MB/s | 127 kB 00:00 (35/78): perl-URI-5.27-3.el10.noarch.rpm 3.6 MB/s | 134 kB 00:00 (36/78): perl-parent-0.241-512.el10.noarch.rpm 880 kB/s | 16 kB 00:00 (37/78): perl-podlators-5.01-511.el10.noarch.rp 6.6 MB/s | 124 kB 00:00 (38/78): cmake-filesystem-3.31.8-1.el10.x86_64. 58 kB/s | 21 kB 00:00 (39/78): annobin-docs-13.02-2.el10.noarch.rpm 184 kB/s | 87 kB 00:00 (40/78): annobin-plugin-gcc-13.02-2.el10.x86_64 1.4 MB/s | 997 kB 00:00 (41/78): gcc-plugin-annobin-14.3.1-4.2.el10.x86 168 kB/s | 69 kB 00:00 (42/78): cpp-14.3.1-4.2.el10.x86_64.rpm 15 MB/s | 13 MB 00:00 (43/78): gcc-14.3.1-4.2.el10.x86_64.rpm 38 MB/s | 38 MB 00:00 (44/78): glibc-devel-2.39-99.el10.x86_64.rpm 979 kB/s | 598 kB 00:00 (45/78): libmpc-1.3.1-7.el10.x86_64.rpm 173 kB/s | 71 kB 00:00 (46/78): kernel-headers-6.12.0-191.el10.x86_64. 4.2 MB/s | 3.1 MB 00:00 (47/78): libxcrypt-devel-4.4.36-10.el10.x86_64. 86 kB/s | 30 kB 00:00 (48/78): ncurses-c++-libs-6.4-14.20240127.el10. 108 kB/s | 39 kB 00:00 (49/78): perl-AutoLoader-5.74-514.el10.noarch.r 64 kB/s | 22 kB 00:00 (50/78): ncurses-devel-6.4-14.20240127.el10.x86 1.2 MB/s | 753 kB 00:00 (51/78): perl-B-1.89-514.el10.x86_64.rpm 364 kB/s | 178 kB 00:00 (52/78): perl-Class-Struct-0.68-514.el10.noarch 67 kB/s | 23 kB 00:00 (53/78): perl-DynaLoader-1.56-514.el10.x86_64.r 77 kB/s | 27 kB 00:00 (54/78): perl-Errno-1.38-514.el10.x86_64.rpm 55 kB/s | 16 kB 00:00 (55/78): perl-Fcntl-1.18-514.el10.x86_64.rpm 87 kB/s | 30 kB 00:00 (56/78): perl-File-Basename-2.86-514.el10.noarc 54 kB/s | 18 kB 00:00 (57/78): perl-File-Path-2.18-512.el10.noarch.rp 98 kB/s | 35 kB 00:00 (58/78): perl-File-stat-1.14-514.el10.noarch.rp 53 kB/s | 18 kB 00:00 (59/78): perl-FileHandle-2.05-514.el10.noarch.r 57 kB/s | 16 kB 00:00 (60/78): perl-FindBin-1.54-514.el10.noarch.rpm 52 kB/s | 15 kB 00:00 (61/78): perl-Getopt-Std-1.14-514.el10.noarch.r 57 kB/s | 16 kB 00:00 (62/78): perl-IPC-Open3-1.22-514.el10.noarch.rp 66 kB/s | 23 kB 00:00 (63/78): perl-IO-1.55-514.el10.x86_64.rpm 189 kB/s | 81 kB 00:00 (64/78): perl-SelectSaver-1.02-514.el10.noarch. 44 kB/s | 12 kB 00:00 (65/78): perl-Net-SSLeay-1.94-8.el10.x86_64.rpm 658 kB/s | 380 kB 00:00 (66/78): perl-POSIX-2.20-514.el10.x86_64.rpm 218 kB/s | 97 kB 00:00 (67/78): perl-Symbol-1.09-514.el10.noarch.rpm 52 kB/s | 15 kB 00:00 (68/78): perl-base-2.27-514.el10.noarch.rpm 50 kB/s | 17 kB 00:00 (69/78): perl-if-0.61.000-514.el10.noarch.rpm 52 kB/s | 15 kB 00:00 (70/78): perl-lib-0.65-514.el10.x86_64.rpm 54 kB/s | 16 kB 00:00 (71/78): perl-interpreter-5.40.2-514.el10.x86_6 176 kB/s | 73 kB 00:00 (72/78): perl-locale-1.12-514.el10.noarch.rpm 50 kB/s | 14 kB 00:00 (73/78): perl-mro-1.29-514.el10.x86_64.rpm 88 kB/s | 31 kB 00:00 (74/78): perl-libs-5.40.2-514.el10.x86_64.rpm 3.3 MB/s | 2.4 MB 00:00 (75/78): perl-overload-1.37-514.el10.noarch.rpm 122 kB/s | 46 kB 00:00 (76/78): perl-overloading-0.02-514.el10.noarch. 49 kB/s | 14 kB 00:00 (77/78): perl-vars-1.05-514.el10.noarch.rpm 49 kB/s | 14 kB 00:00 (78/78): zlib-ng-compat-devel-2.2.3-3.el10.x86_ 100 kB/s | 36 kB 00:00 -------------------------------------------------------------------------------- Total 9.7 MB/s | 67 MB 00:06 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.3.1-7.el10.x86_64 1/78 Installing : htslib-1.23-1.el10.x86_64 2/78 Installing : cpp-14.3.1-4.2.el10.x86_64 3/78 Installing : ncurses-c++-libs-6.4-14.20240127.el10.x86_64 4/78 Installing : kernel-headers-6.12.0-191.el10.x86_64 5/78 Installing : libxcrypt-devel-4.4.36-10.el10.x86_64 6/78 Installing : glibc-devel-2.39-99.el10.x86_64 7/78 Installing : cmake-filesystem-3.31.8-1.el10.x86_64 8/78 Installing : annobin-docs-13.02-2.el10.noarch 9/78 Installing : ncurses-6.4-14.20240127.el10.x86_64 10/78 Installing : make-1:4.4.1-9.el10.x86_64 11/78 Installing : gcc-14.3.1-4.2.el10.x86_64 12/78 Running scriptlet: gcc-14.3.1-4.2.el10.x86_64 12/78 Running scriptlet: groff-base-1.23.0-10.el10.x86_64 13/78 Installing : groff-base-1.23.0-10.el10.x86_64 13/78 Running scriptlet: groff-base-1.23.0-10.el10.x86_64 13/78 Installing : perl-Digest-1.20-511.el10.noarch 14/78 Installing : perl-Digest-MD5-2.59-6.el10.x86_64 15/78 Installing : perl-B-1.89-514.el10.x86_64 16/78 Installing : perl-FileHandle-2.05-514.el10.noarch 17/78 Installing : perl-Data-Dumper-2.189-512.el10.x86_64 18/78 Installing : perl-libnet-3.15-512.el10.noarch 19/78 Installing : perl-AutoLoader-5.74-514.el10.noarch 20/78 Installing : perl-URI-5.27-3.el10.noarch 21/78 Installing : perl-Text-Tabs+Wrap-2024.001-511.el10.noarch 22/78 Installing : perl-Time-Local-2:1.350-511.el10.noarch 23/78 Installing : perl-Mozilla-CA-20231213-5.el10.noarch 24/78 Installing : perl-if-0.61.000-514.el10.noarch 25/78 Installing : perl-locale-1.12-514.el10.noarch 26/78 Installing : perl-IO-Socket-IP-0.42-512.el10.noarch 27/78 Installing : perl-Pod-Escapes-1:1.07-511.el10.noarch 28/78 Installing : perl-File-Path-2.18-512.el10.noarch 29/78 Installing : perl-IO-Socket-SSL-2.085-3.el10.noarch 30/78 Installing : perl-Net-SSLeay-1.94-8.el10.x86_64 31/78 Installing : perl-Term-ANSIColor-5.01-512.el10.noarch 32/78 Installing : perl-Class-Struct-0.68-514.el10.noarch 33/78 Installing : perl-POSIX-2.20-514.el10.x86_64 34/78 Installing : perl-IPC-Open3-1.22-514.el10.noarch 35/78 Installing : perl-Term-Cap-1.18-511.el10.noarch 36/78 Installing : perl-File-Temp-1:0.231.100-512.el10.noarch 37/78 Installing : perl-HTTP-Tiny-0.088-512.el10.noarch 38/78 Installing : perl-Pod-Simple-1:3.45-511.el10.noarch 39/78 Installing : perl-Socket-4:2.038-511.el10.x86_64 40/78 Installing : perl-SelectSaver-1.02-514.el10.noarch 41/78 Installing : perl-Symbol-1.09-514.el10.noarch 42/78 Installing : perl-File-stat-1.14-514.el10.noarch 43/78 Installing : perl-podlators-1:5.01-511.el10.noarch 44/78 Installing : perl-Pod-Perldoc-3.28.01-512.el10.noarch 45/78 Installing : perl-Text-ParseWords-3.31-511.el10.noarch 46/78 Installing : perl-Fcntl-1.18-514.el10.x86_64 47/78 Installing : perl-base-2.27-514.el10.noarch 48/78 Installing : perl-mro-1.29-514.el10.x86_64 49/78 Installing : perl-IO-1.55-514.el10.x86_64 50/78 Installing : perl-overloading-0.02-514.el10.noarch 51/78 Installing : perl-Pod-Usage-4:2.03-511.el10.noarch 52/78 Installing : perl-MIME-Base64-3.16-511.el10.x86_64 53/78 Installing : perl-Scalar-List-Utils-5:1.63-511.el10.x86_64 54/78 Installing : perl-constant-1.33-512.el10.noarch 55/78 Installing : perl-parent-1:0.241-512.el10.noarch 56/78 Installing : perl-Errno-1.38-514.el10.x86_64 57/78 Installing : perl-File-Basename-2.86-514.el10.noarch 58/78 Installing : perl-Getopt-Std-1.14-514.el10.noarch 59/78 Installing : perl-Storable-1:3.32-511.el10.x86_64 60/78 Installing : perl-overload-1.37-514.el10.noarch 61/78 Installing : perl-vars-1.05-514.el10.noarch 62/78 Installing : perl-Getopt-Long-1:2.58-3.el10.noarch 63/78 Installing : perl-Carp-1.54-511.el10.noarch 64/78 Installing : perl-Exporter-5.78-511.el10.noarch 65/78 Installing : perl-PathTools-3.91-512.el10.x86_64 66/78 Installing : perl-DynaLoader-1.56-514.el10.x86_64 67/78 Installing : perl-Encode-4:3.21-511.el10.x86_64 68/78 Installing : perl-libs-4:5.40.2-514.el10.x86_64 69/78 Installing : perl-interpreter-4:5.40.2-514.el10.x86_64 70/78 Installing : perl-FindBin-1.54-514.el10.noarch 71/78 Installing : perl-lib-0.65-514.el10.x86_64 72/78 Installing : annobin-plugin-gcc-13.02-2.el10.x86_64 73/78 Running scriptlet: annobin-plugin-gcc-13.02-2.el10.x86_64 73/78 Installing : gcc-plugin-annobin-14.3.1-4.2.el10.x86_64 74/78 Running scriptlet: gcc-plugin-annobin-14.3.1-4.2.el10.x86_64 74/78 Installing : zlib-ng-compat-devel-2.2.3-3.el10.x86_64 75/78 Installing : ncurses-devel-6.4-14.20240127.el10.x86_64 76/78 Installing : htslib-devel-1.23-1.el10.x86_64 77/78 Installing : htslib-tools-1.23-1.el10.x86_64 78/78 Running scriptlet: htslib-tools-1.23-1.el10.x86_64 78/78 Installed: annobin-docs-13.02-2.el10.noarch annobin-plugin-gcc-13.02-2.el10.x86_64 cmake-filesystem-3.31.8-1.el10.x86_64 cpp-14.3.1-4.2.el10.x86_64 gcc-14.3.1-4.2.el10.x86_64 gcc-plugin-annobin-14.3.1-4.2.el10.x86_64 glibc-devel-2.39-99.el10.x86_64 groff-base-1.23.0-10.el10.x86_64 htslib-1.23-1.el10.x86_64 htslib-devel-1.23-1.el10.x86_64 htslib-tools-1.23-1.el10.x86_64 kernel-headers-6.12.0-191.el10.x86_64 libmpc-1.3.1-7.el10.x86_64 libxcrypt-devel-4.4.36-10.el10.x86_64 make-1:4.4.1-9.el10.x86_64 ncurses-6.4-14.20240127.el10.x86_64 ncurses-c++-libs-6.4-14.20240127.el10.x86_64 ncurses-devel-6.4-14.20240127.el10.x86_64 perl-AutoLoader-5.74-514.el10.noarch perl-B-1.89-514.el10.x86_64 perl-Carp-1.54-511.el10.noarch perl-Class-Struct-0.68-514.el10.noarch perl-Data-Dumper-2.189-512.el10.x86_64 perl-Digest-1.20-511.el10.noarch perl-Digest-MD5-2.59-6.el10.x86_64 perl-DynaLoader-1.56-514.el10.x86_64 perl-Encode-4:3.21-511.el10.x86_64 perl-Errno-1.38-514.el10.x86_64 perl-Exporter-5.78-511.el10.noarch perl-Fcntl-1.18-514.el10.x86_64 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.x86_64 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.x86_64 perl-Mozilla-CA-20231213-5.el10.noarch perl-Net-SSLeay-1.94-8.el10.x86_64 perl-POSIX-2.20-514.el10.x86_64 perl-PathTools-3.91-512.el10.x86_64 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.x86_64 perl-SelectSaver-1.02-514.el10.noarch perl-Socket-4:2.038-511.el10.x86_64 perl-Storable-1:3.32-511.el10.x86_64 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.x86_64 perl-lib-0.65-514.el10.x86_64 perl-libnet-3.15-512.el10.noarch perl-libs-4:5.40.2-514.el10.x86_64 perl-locale-1.12-514.el10.noarch perl-mro-1.29-514.el10.x86_64 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.x86_64 Complete! Building target platforms: x86_64 Building for target x86_64 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 117 kB/s | 1.5 kB 00:00 CentOS Stream 10 - BaseOS 97 kB/s | 4.5 kB 00:00 CentOS Stream 10 - AppStream 75 kB/s | 5.5 kB 00:00 CentOS Stream 10 - CRB 55 kB/s | 4.4 kB 00:00 CentOS Stream 10 - Extras packages 95 kB/s | 7.3 kB 00:00 Extra Packages for Enterprise Linux 10 - x86_64 140 kB/s | 34 kB 00:00 Package gcc-14.3.1-4.2.el10.x86_64 is already installed. Package htslib-devel-1.23-1.el10.x86_64 is already installed. Package htslib-tools-1.23-1.el10.x86_64 is already installed. Package make-1:4.4.1-9.el10.x86_64 is already installed. Package ncurses-devel-6.4-14.20240127.el10.x86_64 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.x86_64 is already installed. Package perl-interpreter-4:5.40.2-514.el10.x86_64 is already installed. Package zlib-ng-compat-devel-2.2.3-3.el10.x86_64 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: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1769040000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.sxxAZ2 + 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.akLqci + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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=x86_64-redhat-linux --host=x86_64-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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' '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 x86_64-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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 "' >> 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I. -I./lz4 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.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-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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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/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/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/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/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/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_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/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/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/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.RFHeov + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64 ++ dirname /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64 + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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.x86_64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/share/man/man1 /usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/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.x86_64/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.x86_64/usr/bin /usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/share/man/man1 ++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/zoom2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/blast2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/bowtie2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/export2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/fasta-sanitize.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/interpolate_sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/novo2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/plot-ampliconstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/plot-bamstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/psl2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/sam2vcf.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/samtools.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/seq_cache_populate.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/soap2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/wgsim_eval.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/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.x86_64 --unique-debug-src-base samtools-1.23-1.el10.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -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.x86_64 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.4Ob0O2 + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 (0x00007fec49fbb000) + 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/OvWtArnPpB/bgzip.dat.gz .. ok bgzip -c -b 979200 -s 6 /tmp/OvWtArnPpB/bgzip.dat.gz .. ok bgzip -c -b 652804 -s 6 /tmp/OvWtArnPpB/bgzip.dat.gz .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/OvWtArnPpB/faidx.fa 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/OvWtArnPpB/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/OvWtArnPpB/faidx.fa 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/OvWtArnPpB/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/OvWtArnPpB/faidx.fa 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/OvWtArnPpB/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/OvWtArnPpB/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/OvWtArnPpB/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/OvWtArnPpB/fqidx.fq 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/OvWtArnPpB/fqidx.fq.gz 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/OvWtArnPpB/fqidx.fq 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/OvWtArnPpB/fqidx.fq.gz 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/OvWtArnPpB/fqidx.fq 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/OvWtArnPpB/fqidx.fq.gz 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/OvWtArnPpB/fqidx.fq 1:99998-100007 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view /tmp/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/auto_indexed.csi && cat /tmp/OvWtArnPpB/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/OvWtArnPpB/auto_indexed.crai && cat /tmp/OvWtArnPpB/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/OvWtArnPpB/auto_indexed.csi && cat /tmp/OvWtArnPpB/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 /tmp/OvWtArnPpB/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 /tmp/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/auto_indexed.csi && cat /tmp/OvWtArnPpB/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/OvWtArnPpB/auto_indexed.crai && cat /tmp/OvWtArnPpB/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/OvWtArnPpB/auto_indexed.csi && cat /tmp/OvWtArnPpB/auto_indexed.csi .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/OvWtArnPpB/mpileup.bam.list -f /tmp/OvWtArnPpB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/OvWtArnPpB/mpileup.cram.list -f /tmp/OvWtArnPpB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/OvWtArnPpB/mpileup.bam.urllist -f /tmp/OvWtArnPpB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/OvWtArnPpB/mpileup.cram.urllist -f /tmp/OvWtArnPpB/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/OvWtArnPpB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/OvWtArnPpB/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/OvWtArnPpB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/OvWtArnPpB/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/OvWtArnPpB/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/OvWtArnPpB/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/OvWtArnPpB/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/OvWtArnPpB/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/OvWtArnPpB/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/OvWtArnPpB/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/OvWtArnPpB/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/OvWtArnPpB/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/OvWtArnPpB/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/OvWtArnPpB/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/OvWtArnPpB/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/OvWtArnPpB/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/OvWtArnPpB/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/OvWtArnPpB/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/OvWtArnPpB/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/OvWtArnPpB/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/OvWtArnPpB/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/OvWtArnPpB/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/OvWtArnPpB/view.001.forn (SAM input) .. ok 68: Count -N /tmp/OvWtArnPpB/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/OvWtArnPpB/view.001.forn (BAM input) .. ok 70: Count -N /tmp/OvWtArnPpB/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/OvWtArnPpB/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/OvWtArnPpB/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/OvWtArnPpB/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/OvWtArnPpB/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/OvWtArnPpB/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/OvWtArnPpB/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/OvWtArnPpB/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/OvWtArnPpB/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/OvWtArnPpB/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/OvWtArnPpB/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/OvWtArnPpB/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/OvWtArnPpB/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/OvWtArnPpB/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/OvWtArnPpB/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/OvWtArnPpB/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/OvWtArnPpB/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/OvWtArnPpB/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/OvWtArnPpB/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/OvWtArnPpB/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/OvWtArnPpB/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/OvWtArnPpB/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/OvWtArnPpB/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/OvWtArnPpB/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/OvWtArnPpB/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/OvWtArnPpB/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/OvWtArnPpB/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/OvWtArnPpB/view.test115.sam -h -d TGCA /tmp/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/view.test117.sam -h -d TGCA /tmp/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/view.test119.sam -h -d TGCA /tmp/OvWtArnPpB/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/OvWtArnPpB/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/OvWtArnPpB/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/OvWtArnPpB/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/OvWtArnPpB/view.test121.sam -h -D BClong:/tmp/OvWtArnPpB/view.001.fobc /tmp/OvWtArnPpB/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/OvWtArnPpB/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/OvWtArnPpB/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/OvWtArnPpB/view.001.fobc /tmp/OvWtArnPpB/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/OvWtArnPpB/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/OvWtArnPpB/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/OvWtArnPpB/view.test123.sam -h -D BClong:/tmp/OvWtArnPpB/view.001.fobc /tmp/OvWtArnPpB/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/OvWtArnPpB/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/OvWtArnPpB/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/OvWtArnPpB/view.001.fobc /tmp/OvWtArnPpB/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/OvWtArnPpB/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/OvWtArnPpB/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/OvWtArnPpB/view.test125.sam -h -D BClong:/tmp/OvWtArnPpB/view.001.fobc /tmp/OvWtArnPpB/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/OvWtArnPpB/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/OvWtArnPpB/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/OvWtArnPpB/view.001.fobc /tmp/OvWtArnPpB/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/OvWtArnPpB/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/bam2fq.discard.s.fq -0 /tmp/OvWtArnPpB/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/OvWtArnPpB/bam2fq.discard.s.fq -0 /tmp/OvWtArnPpB/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/YSLUsIvNzj - /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/OvWtArnPpB/merge.tag.1.bam /tmp/OvWtArnPpB/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/OvWtArnPpB/merge.tag.3.bam /tmp/OvWtArnPpB/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/OvWtArnPpB/merge.bed.1.bam /tmp/OvWtArnPpB/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/S_4qtLkSRX - /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/OvWtArnPpB/merge.tag.1.bam /tmp/OvWtArnPpB/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/OvWtArnPpB/merge.tag.3.bam /tmp/OvWtArnPpB/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/OvWtArnPpB/merge.bed.1.bam /tmp/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /tmp/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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/OvWtArnPpB/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.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.EbEtp0 + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + DOCDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/share/doc/samtools + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/share/doc/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/AUTHORS /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/share/doc/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/ChangeLog.old /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/share/doc/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/NEWS.md /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/share/doc/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/examples /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/share/doc/samtools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.GZJNL1 + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/share/licenses/samtools + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/share/licenses/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/LICENSE /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64/usr/share/licenses/samtools + RPM_EC=0 ++ jobs -p + exit 0 Provides: samtools = 1.23-1.el10 samtools(x86-64) = 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 libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(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_2.2.5)(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.x86_64 Provides: samtools-debugsource = 1.23-1.el10 samtools-debugsource(x86-64) = 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.x86_64 Provides: debuginfo(build-id) = 00fba5601bb7aab69e8b5cc7fd82ad0fd4343820 debuginfo(build-id) = 05f1c5a53eaa3a8ca1895c2208c5171a8e8c0c6c debuginfo(build-id) = 325b8b379ed6bc8125efbad6066cf3d85ddc8e6a debuginfo(build-id) = 60633f809adbe85ec036b0b4ea6aa0b8d1176f46 debuginfo(build-id) = cdc2fbd1627e297c40869608a83155cba7a63e47 debuginfo(build-id) = e3e711e0f13bdfa1b75fd3dbb00db969199b834c debuginfo(build-id) = fe1589e904a4e0f77aa05a360afd52116dea41f5 samtools-debuginfo = 1.23-1.el10 samtools-debuginfo(x86-64) = 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(x86-64) = 1.23-1.el10 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64 Wrote: /builddir/build/RPMS/samtools-1.23-1.el10.x86_64.rpm Wrote: /builddir/build/RPMS/samtools-debugsource-1.23-1.el10.x86_64.rpm Wrote: /builddir/build/RPMS/samtools-debuginfo-1.23-1.el10.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Khd0QI + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.23-1.el10.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.JDYdqN + 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-x86_64-1769501915.991329/root/var/log/dnf.rpm.log /var/lib/mock/centos-stream+epel-10-x86_64-1769501915.991329/root/var/log/dnf.librepo.log /var/lib/mock/centos-stream+epel-10-x86_64-1769501915.991329/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 1 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", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "x86_64" }, { "name": "samtools-debugsource", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "x86_64" }, { "name": "samtools-debuginfo", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "x86_64" }, { "name": "samtools", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "src" } ] } RPMResults finished