Warning: Permanently added '2620:52:6:1161:dead:beef:cafe:c194' (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/10066888-epel-10-ppc64le --chroot epel-10-ppc64le Version: 1.6 PID: 16316 Logging PID: 16318 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 10066888, 'buildroot_pkgs': [], 'chroot': 'epel-10-ppc64le', 'enable_net': False, 'fedora_review': False, 'git_hash': '624052c1792453848c83aeb6f9b9daebd1bdd335', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ron/staging/samtools', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'samtools', 'package_version': '1.23-1', 'project_dirname': 'staging', 'project_name': 'staging', 'project_owner': 'ron', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ron/staging/epel-10-ppc64le/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'ron/staging--ron', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'ron', 'tags': ['arch_power9'], 'task_id': '10066888-epel-10-ppc64le', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ron/staging/samtools /var/lib/copr-rpmbuild/workspace/workdir-g0nsw1_5/samtools --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ron/staging/samtools', '/var/lib/copr-rpmbuild/workspace/workdir-g0nsw1_5/samtools', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-g0nsw1_5/samtools'... Running: git checkout 624052c1792453848c83aeb6f9b9daebd1bdd335 -- cmd: ['git', 'checkout', '624052c1792453848c83aeb6f9b9daebd1bdd335', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-g0nsw1_5/samtools rc: 0 stdout: stderr: Note: switching to '624052c1792453848c83aeb6f9b9daebd1bdd335'. 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 624052c automatic import of samtools Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-g0nsw1_5/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/staging/samtools/samtools-1.23.tar.bz2/md5/7ce93103e5a3796c0009f879853837bb/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-g0nsw1_5/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-g0nsw1_5/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769509936.247694 -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-g0nsw1_5/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-g0nsw1_5/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769509936.247694 -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-g0nsw1_5/samtools/samtools.spec) Config(centos-stream+epel-10-ppc64le) 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-ppc64le-bootstrap-1769509936.247694/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-4298b3ec-87c3-4eab-813b-0c6f4134a9cc INFO: Checking that 69646e6961119ce7a22235fb4c52fba809be016ae0e8f6ef0dcc1b6956ec7eb5 image matches host's architecture INFO: Copy content of container 69646e6961119ce7a22235fb4c52fba809be016ae0e8f6ef0dcc1b6956ec7eb5 to /var/lib/mock/centos-stream+epel-10-ppc64le-bootstrap-1769509936.247694/root INFO: mounting 69646e6961119ce7a22235fb4c52fba809be016ae0e8f6ef0dcc1b6956ec7eb5 with podman image mount INFO: image 69646e6961119ce7a22235fb4c52fba809be016ae0e8f6ef0dcc1b6956ec7eb5 as /var/lib/containers/storage/overlay/b4199976636f3ad46ae2b6dafc99ba2f52108b45b627bae5ae459cfa6277de10/merged INFO: umounting image 69646e6961119ce7a22235fb4c52fba809be016ae0e8f6ef0dcc1b6956ec7eb5 (/var/lib/containers/storage/overlay/b4199976636f3ad46ae2b6dafc99ba2f52108b45b627bae5ae459cfa6277de10/merged) with podman image umount INFO: Removing image mock-bootstrap-4298b3ec-87c3-4eab-813b-0c6f4134a9cc 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-ppc64le-1769509936.247694/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.ppc64le rpm-sequoia-1.9.0.3-1.el10.ppc64le 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 12 kB/s | 4.6 kB 00:00 CentOS Stream 10 - BaseOS 1.5 MB/s | 4.1 MB 00:02 CentOS Stream 10 - AppStream 3.1 MB/s | 3.4 MB 00:01 CentOS Stream 10 - CRB 191 kB/s | 770 kB 00:04 CentOS Stream 10 - Extras packages 5.5 kB/s | 8.5 kB 00:01 Extra Packages for Enterprise Linux 10 - ppc64l 103 kB/s | 6.1 MB 01:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: bash ppc64le 5.2.26-6.el10 baseos 1.9 M bzip2 ppc64le 1.0.8-25.el10 baseos 55 k centos-stream-release noarch 10.0-19.el10 baseos 30 k coreutils ppc64le 9.5-6.el10 baseos 1.2 M cpio ppc64le 2.15-3.el10 baseos 299 k diffutils ppc64le 3.10-8.el10 baseos 419 k epel-rpm-macros noarch 10-6.el10_2 epel 8.2 k findutils ppc64le 1:4.10.0-5.el10 baseos 567 k gawk ppc64le 5.3.0-6.el10 baseos 1.1 M glibc-minimal-langpack ppc64le 2.39-99.el10 baseos 39 k grep ppc64le 3.11-10.el10 baseos 310 k gzip ppc64le 1.13-3.el10 baseos 173 k info ppc64le 7.1-6.el10 baseos 201 k patch ppc64le 2.7.6-26.el10 appstream 142 k redhat-rpm-config noarch 295-1.el10 appstream 74 k rpm-build ppc64le 4.19.1.1-21.el10 appstream 76 k sed ppc64le 4.9-3.el10 baseos 322 k shadow-utils ppc64le 2:4.15.0-9.el10 baseos 1.4 M tar ppc64le 2:1.35-10.el10 baseos 885 k unzip ppc64le 6.0-69.el10 baseos 192 k util-linux ppc64le 2.40.2-13.el10 baseos 1.3 M which ppc64le 2.21-44.el10 baseos 43 k xz ppc64le 1:5.6.2-4.el10 baseos 484 k Installing dependencies: alternatives ppc64le 1.30-2.el10 baseos 44 k ansible-srpm-macros noarch 1-16.1.el10_0 epel 20 k audit-libs ppc64le 4.0.3-5.el10 baseos 144 k authselect ppc64le 1.5.0-8.el10 baseos 145 k authselect-libs ppc64le 1.5.0-8.el10 baseos 225 k basesystem noarch 11-22.el10 baseos 4.3 k binutils ppc64le 2.41-60.el10 baseos 6.4 M binutils-gold ppc64le 2.41-60.el10 baseos 1.1 M bzip2-libs ppc64le 1.0.8-25.el10 baseos 46 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 ppc64le 9.5-6.el10 baseos 2.1 M cracklib ppc64le 2.9.11-8.el10 baseos 98 k cracklib-dicts ppc64le 2.9.11-8.el10 baseos 3.6 M crypto-policies noarch 20251127-1.git27c2902.el10 baseos 98 k curl ppc64le 8.12.1-4.el10 baseos 222 k cyrus-sasl-lib ppc64le 2.1.28-27.el10 baseos 118 k debugedit ppc64le 5.1-8.el10 appstream 82 k dwz ppc64le 0.16-1.el10 appstream 144 k ed ppc64le 1.20-5.el10 baseos 86 k efi-srpm-macros noarch 6-6.el10 appstream 24 k elfutils ppc64le 0.194-1.el10 baseos 574 k elfutils-debuginfod-client ppc64le 0.194-1.el10 baseos 45 k elfutils-default-yama-scope noarch 0.194-1.el10 baseos 8.3 k elfutils-libelf ppc64le 0.194-1.el10 baseos 207 k elfutils-libs ppc64le 0.194-1.el10 baseos 303 k file ppc64le 5.45-8.el10 baseos 50 k file-libs ppc64le 5.45-8.el10 baseos 775 k filesystem ppc64le 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 ppc64le 16.3-2.el10 appstream 4.5 M gdbm ppc64le 1:1.23-14.el10 baseos 157 k gdbm-libs ppc64le 1:1.23-14.el10 baseos 62 k ghc-srpm-macros noarch 1.9.2-1.el10_0 epel 9.1 k glibc ppc64le 2.39-99.el10 baseos 2.9 M glibc-common ppc64le 2.39-99.el10 baseos 340 k glibc-gconv-extra ppc64le 2.39-99.el10 baseos 1.8 M gmp ppc64le 1:6.2.1-12.el10 baseos 303 k go-srpm-macros noarch 3.8.0-1.el10 appstream 27 k jansson ppc64le 2.14-3.el10 baseos 51 k json-c ppc64le 0.18-3.el10 baseos 50 k kernel-srpm-macros noarch 1.0-27.el10 appstream 8.7 k keyutils-libs ppc64le 1.6.3-5.el10 baseos 34 k krb5-libs ppc64le 1.21.3-8.el10 baseos 845 k libacl ppc64le 2.3.2-4.el10 baseos 28 k libarchive ppc64le 3.7.7-4.el10 baseos 475 k libattr ppc64le 2.5.2-5.el10 baseos 20 k libblkid ppc64le 2.40.2-13.el10 baseos 139 k libbrotli ppc64le 1.1.0-7.el10 baseos 383 k libcap ppc64le 2.69-7.el10 baseos 96 k libcap-ng ppc64le 0.8.4-6.el10 baseos 34 k libcom_err ppc64le 1.47.1-5.el10 baseos 26 k libcurl ppc64le 8.12.1-4.el10 baseos 412 k libeconf ppc64le 0.6.2-4.el10 baseos 37 k libevent ppc64le 2.1.12-16.el10 baseos 275 k libfdisk ppc64le 2.40.2-13.el10 baseos 173 k libffi ppc64le 3.4.4-10.el10 baseos 38 k libgcc ppc64le 14.3.1-4.2.el10 baseos 107 k libgomp ppc64le 14.3.1-4.2.el10 baseos 382 k libidn2 ppc64le 2.3.7-3.el10 baseos 120 k libmount ppc64le 2.40.2-13.el10 baseos 175 k libnghttp2 ppc64le 1.64.0-2.el10 baseos 86 k libpkgconf ppc64le 2.1.0-3.el10 baseos 43 k libpsl ppc64le 0.21.5-6.el10 baseos 67 k libpwquality ppc64le 1.4.5-12.el10 baseos 125 k librtas ppc64le 2.0.6-4.el10 baseos 82 k libselinux ppc64le 3.9-3.el10 baseos 108 k libsemanage ppc64le 3.9-2.el10 baseos 134 k libsepol ppc64le 3.9-1.el10 baseos 376 k libsmartcols ppc64le 2.40.2-13.el10 baseos 89 k libssh ppc64le 0.11.1-3.el10 baseos 262 k libssh-config noarch 0.11.1-3.el10 baseos 8.4 k libstdc++ ppc64le 14.3.1-4.2.el10 baseos 1.0 M libtasn1 ppc64le 4.20.0-1.el10 baseos 80 k libunistring ppc64le 1.1-10.el10 baseos 553 k libutempter ppc64le 1.2.1-15.el10 baseos 28 k libuuid ppc64le 2.40.2-13.el10 baseos 30 k libverto ppc64le 0.3.2-10.el10 baseos 23 k libxcrypt ppc64le 4.4.36-10.el10 baseos 131 k libxml2 ppc64le 2.12.5-9.el10 baseos 762 k libzstd ppc64le 1.5.5-9.el10 baseos 332 k lua-libs ppc64le 5.4.6-7.el10 baseos 148 k lua-srpm-macros noarch 1-15.el10 appstream 9.8 k lz4-libs ppc64le 1.9.4-8.el10 baseos 87 k mpfr ppc64le 4.2.1-6.el10 baseos 334 k ncurses-base noarch 6.4-14.20240127.el10 baseos 100 k ncurses-libs ppc64le 6.4-14.20240127.el10 baseos 380 k ocaml-srpm-macros noarch 10-4.el10 appstream 10 k openblas-srpm-macros noarch 2-19.el10 appstream 8.7 k openldap ppc64le 2.6.10-1.el10 baseos 266 k openssl-fips-provider ppc64le 1:3.5.1-6.el10 baseos 788 k openssl-libs ppc64le 1:3.5.1-6.el10 baseos 2.4 M p11-kit ppc64le 0.26.1-1.el10 baseos 553 k p11-kit-trust ppc64le 0.26.1-1.el10 baseos 156 k package-notes-srpm-macros noarch 0.5-13.el10 appstream 10 k pam ppc64le 1.6.1-9.el10 baseos 620 k pam-libs ppc64le 1.6.1-9.el10 baseos 61 k pcre2 ppc64le 10.44-1.el10.3 baseos 252 k pcre2-syntax noarch 10.44-1.el10.3 baseos 151 k perl-srpm-macros noarch 1-57.el10 appstream 9.5 k pkgconf ppc64le 2.1.0-3.el10 baseos 45 k pkgconf-m4 noarch 2.1.0-3.el10 baseos 15 k pkgconf-pkg-config ppc64le 2.1.0-3.el10 baseos 11 k popt ppc64le 1.19-8.el10 baseos 70 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 ppc64le 8.2-11.el10 baseos 229 k rpm ppc64le 4.19.1.1-21.el10 baseos 563 k rpm-build-libs ppc64le 4.19.1.1-21.el10 baseos 98 k rpm-libs ppc64le 4.19.1.1-21.el10 baseos 348 k rpm-sequoia ppc64le 1.9.0.3-1.el10 baseos 1.6 M 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 ppc64le 3.46.1-5.el10 baseos 829 k systemd-libs ppc64le 257-21.el10 baseos 859 k util-linux-core ppc64le 2.40.2-13.el10 baseos 566 k xz-libs ppc64le 1:5.6.2-4.el10 baseos 124 k zip ppc64le 3.0-45.el10 baseos 277 k zlib-ng-compat ppc64le 2.2.3-3.el10 baseos 77 k zstd ppc64le 1.5.5-9.el10 baseos 495 k Transaction Summary ================================================================================ Install 148 Packages Total download size: 64 M Installed size: 239 M Downloading Packages: (1/148): alternatives-1.30-2.el10.ppc64le.rpm 51 kB/s | 44 kB 00:00 (2/148): audit-libs-4.0.3-5.el10.ppc64le.rpm 122 kB/s | 144 kB 00:01 (3/148): authselect-1.5.0-8.el10.ppc64le.rpm 114 kB/s | 145 kB 00:01 (4/148): basesystem-11-22.el10.noarch.rpm 38 kB/s | 4.3 kB 00:00 (5/148): authselect-libs-1.5.0-8.el10.ppc64le.r 352 kB/s | 225 kB 00:00 (6/148): binutils-gold-2.41-60.el10.ppc64le.rpm 828 kB/s | 1.1 MB 00:01 (7/148): bzip2-1.0.8-25.el10.ppc64le.rpm 447 kB/s | 55 kB 00:00 (8/148): bzip2-libs-1.0.8-25.el10.ppc64le.rpm 385 kB/s | 46 kB 00:00 (9/148): bash-5.2.26-6.el10.ppc64le.rpm 743 kB/s | 1.9 MB 00:02 (10/148): ca-certificates-2025.2.80_v9.0.305-10 1.4 MB/s | 1.1 MB 00:00 (11/148): centos-gpg-keys-10.0-19.el10.noarch.r 176 kB/s | 26 kB 00:00 (12/148): centos-stream-release-10.0-19.el10.no 282 kB/s | 30 kB 00:00 (13/148): centos-stream-repos-10.0-19.el10.noar 114 kB/s | 12 kB 00:00 (14/148): coreutils-9.5-6.el10.ppc64le.rpm 1.5 MB/s | 1.2 MB 00:00 (15/148): cpio-2.15-3.el10.ppc64le.rpm 1.2 MB/s | 299 kB 00:00 (16/148): cracklib-2.9.11-8.el10.ppc64le.rpm 748 kB/s | 98 kB 00:00 (17/148): binutils-2.41-60.el10.ppc64le.rpm 1.5 MB/s | 6.4 MB 00:04 (18/148): coreutils-common-9.5-6.el10.ppc64le.r 1.5 MB/s | 2.1 MB 00:01 (19/148): crypto-policies-20251127-1.git27c2902 755 kB/s | 98 kB 00:00 (20/148): curl-8.12.1-4.el10.ppc64le.rpm 1.6 MB/s | 222 kB 00:00 (21/148): cyrus-sasl-lib-2.1.28-27.el10.ppc64le 684 kB/s | 118 kB 00:00 (22/148): diffutils-3.10-8.el10.ppc64le.rpm 1.7 MB/s | 419 kB 00:00 (23/148): ed-1.20-5.el10.ppc64le.rpm 541 kB/s | 86 kB 00:00 (24/148): elfutils-debuginfod-client-0.194-1.el 300 kB/s | 45 kB 00:00 (25/148): elfutils-default-yama-scope-0.194-1.e 73 kB/s | 8.3 kB 00:00 (26/148): elfutils-0.194-1.el10.ppc64le.rpm 1.6 MB/s | 574 kB 00:00 (27/148): elfutils-libs-0.194-1.el10.ppc64le.rp 1.3 MB/s | 303 kB 00:00 (28/148): file-5.45-8.el10.ppc64le.rpm 397 kB/s | 50 kB 00:00 (29/148): cracklib-dicts-2.9.11-8.el10.ppc64le. 2.3 MB/s | 3.6 MB 00:01 (30/148): elfutils-libelf-0.194-1.el10.ppc64le. 376 kB/s | 207 kB 00:00 (31/148): file-libs-5.45-8.el10.ppc64le.rpm 2.2 MB/s | 775 kB 00:00 (32/148): gawk-5.3.0-6.el10.ppc64le.rpm 2.4 MB/s | 1.1 MB 00:00 (33/148): gdbm-1.23-14.el10.ppc64le.rpm 1.2 MB/s | 157 kB 00:00 (34/148): gdbm-libs-1.23-14.el10.ppc64le.rpm 496 kB/s | 62 kB 00:00 (35/148): filesystem-3.18-17.el10.ppc64le.rpm 3.2 MB/s | 4.8 MB 00:01 (36/148): glibc-common-2.39-99.el10.ppc64le.rpm 2.4 MB/s | 340 kB 00:00 (37/148): findutils-4.10.0-5.el10.ppc64le.rpm 299 kB/s | 567 kB 00:01 (38/148): glibc-minimal-langpack-2.39-99.el10.p 370 kB/s | 39 kB 00:00 (39/148): glibc-gconv-extra-2.39-99.el10.ppc64l 3.6 MB/s | 1.8 MB 00:00 (40/148): grep-3.11-10.el10.ppc64le.rpm 2.1 MB/s | 310 kB 00:00 (41/148): gmp-6.2.1-12.el10.ppc64le.rpm 860 kB/s | 303 kB 00:00 (42/148): gzip-1.13-3.el10.ppc64le.rpm 1.2 MB/s | 173 kB 00:00 (43/148): jansson-2.14-3.el10.ppc64le.rpm 400 kB/s | 51 kB 00:00 (44/148): json-c-0.18-3.el10.ppc64le.rpm 408 kB/s | 50 kB 00:00 (45/148): info-7.1-6.el10.ppc64le.rpm 696 kB/s | 201 kB 00:00 (46/148): keyutils-libs-1.6.3-5.el10.ppc64le.rp 273 kB/s | 34 kB 00:00 (47/148): libacl-2.3.2-4.el10.ppc64le.rpm 225 kB/s | 28 kB 00:00 (48/148): krb5-libs-1.21.3-8.el10.ppc64le.rpm 1.1 MB/s | 845 kB 00:00 (49/148): glibc-2.39-99.el10.ppc64le.rpm 1.1 MB/s | 2.9 MB 00:02 (50/148): libattr-2.5.2-5.el10.ppc64le.rpm 159 kB/s | 20 kB 00:00 (51/148): libblkid-2.40.2-13.el10.ppc64le.rpm 1.0 MB/s | 139 kB 00:00 (52/148): libcap-2.69-7.el10.ppc64le.rpm 664 kB/s | 96 kB 00:00 (53/148): libcap-ng-0.8.4-6.el10.ppc64le.rpm 247 kB/s | 34 kB 00:00 (54/148): libbrotli-1.1.0-7.el10.ppc64le.rpm 839 kB/s | 383 kB 00:00 (55/148): libcom_err-1.47.1-5.el10.ppc64le.rpm 211 kB/s | 26 kB 00:00 (56/148): 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libzstd-1.5.5-9.el10.ppc64le.rpm 604 kB/s | 332 kB 00:00 (86/148): lz4-libs-1.9.4-8.el10.ppc64le.rpm 618 kB/s | 87 kB 00:00 (87/148): libunistring-1.1-10.el10.ppc64le.rpm 350 kB/s | 553 kB 00:01 (88/148): ncurses-base-6.4-14.20240127.el10.noa 792 kB/s | 100 kB 00:00 (89/148): mpfr-4.2.1-6.el10.ppc64le.rpm 758 kB/s | 334 kB 00:00 (90/148): openldap-2.6.10-1.el10.ppc64le.rpm 753 kB/s | 266 kB 00:00 (91/148): ncurses-libs-6.4-14.20240127.el10.ppc 708 kB/s | 380 kB 00:00 (92/148): openssl-fips-provider-3.5.1-6.el10.pp 1.0 MB/s | 788 kB 00:00 (93/148): p11-kit-0.26.1-1.el10.ppc64le.rpm 858 kB/s | 553 kB 00:00 (94/148): p11-kit-trust-0.26.1-1.el10.ppc64le.r 679 kB/s | 156 kB 00:00 (95/148): pam-libs-1.6.1-9.el10.ppc64le.rpm 507 kB/s | 61 kB 00:00 (96/148): pcre2-10.44-1.el10.3.ppc64le.rpm 1.1 MB/s | 252 kB 00:00 (97/148): pam-1.6.1-9.el10.ppc64le.rpm 1.1 MB/s | 620 kB 00:00 (98/148): pcre2-syntax-10.44-1.el10.3.noarch.rp 943 kB/s | 151 kB 00:00 (99/148): pkgconf-2.1.0-3.el10.ppc64le.rpm 336 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openssl-libs-3.5.1-6.el10.ppc64le.rp 621 kB/s | 2.4 MB 00:03 (115/148): tar-1.35-10.el10.ppc64le.rpm 2.0 MB/s | 885 kB 00:00 (116/148): unzip-6.0-69.el10.ppc64le.rpm 301 kB/s | 192 kB 00:00 (117/148): util-linux-core-2.40.2-13.el10.ppc64 1.7 MB/s | 566 kB 00:00 (118/148): which-2.21-44.el10.ppc64le.rpm 346 kB/s | 43 kB 00:00 (119/148): xz-5.6.2-4.el10.ppc64le.rpm 2.0 MB/s | 484 kB 00:00 (120/148): util-linux-2.40.2-13.el10.ppc64le.rp 1.3 MB/s | 1.3 MB 00:00 (121/148): xz-libs-5.6.2-4.el10.ppc64le.rpm 364 kB/s | 124 kB 00:00 (122/148): zip-3.0-45.el10.ppc64le.rpm 2.0 MB/s | 277 kB 00:00 (123/148): zlib-ng-compat-2.2.3-3.el10.ppc64le. 566 kB/s | 77 kB 00:00 (124/148): zstd-1.5.5-9.el10.ppc64le.rpm 663 kB/s | 495 kB 00:00 (125/148): debugedit-5.1-8.el10.ppc64le.rpm 97 kB/s | 82 kB 00:00 (126/148): fonts-srpm-macros-2.0.5-18.el10.noar 252 kB/s | 27 kB 00:00 (127/148): forge-srpm-macros-0.4.0-6.el10.noarc 196 kB/s | 21 kB 00:00 (128/148): efi-srpm-macros-6-6.el10.noarch.rpm 72 kB/s | 24 kB 00:00 (129/148): dwz-0.16-1.el10.ppc64le.rpm 135 kB/s | 144 kB 00:01 (130/148): go-srpm-macros-3.8.0-1.el10.noarch.r 243 kB/s | 27 kB 00:00 (131/148): kernel-srpm-macros-1.0-27.el10.noarc 82 kB/s | 8.7 kB 00:00 (132/148): lua-srpm-macros-1-15.el10.noarch.rpm 92 kB/s | 9.8 kB 00:00 (133/148): ocaml-srpm-macros-10-4.el10.noarch.r 92 kB/s | 10 kB 00:00 (134/148): openblas-srpm-macros-2-19.el10.noarc 81 kB/s | 8.7 kB 00:00 (135/148): package-notes-srpm-macros-0.5-13.el1 95 kB/s | 10 kB 00:00 (136/148): perl-srpm-macros-1-57.el10.noarch.rp 89 kB/s | 9.5 kB 00:00 (137/148): pyproject-srpm-macros-1.18.5-1.el10. 124 kB/s | 13 kB 00:00 (138/148): patch-2.7.6-26.el10.ppc64le.rpm 518 kB/s | 142 kB 00:00 (139/148): python-srpm-macros-3.12-11.el10.noar 209 kB/s | 22 kB 00:00 (140/148): qt6-srpm-macros-6.10.1-1.el10.noarch 83 kB/s | 9.1 kB 00:00 (141/148): redhat-rpm-config-295-1.el10.noarch. 409 kB/s | 74 kB 00:00 (142/148): rust-toolset-srpm-macros-1.92.0-1.el 99 kB/s | 11 kB 00:00 (143/148): rpm-build-4.19.1.1-21.el10.ppc64le.r 252 kB/s | 76 kB 00:00 (144/148): gdb-minimal-16.3-2.el10.ppc64le.rpm 903 kB/s | 4.5 MB 00:05 [MIRROR] ansible-srpm-macros-1-16.1.el10_0.noarch.rpm: Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/epel/10.2/Everything/ppc64le/Packages/a/ansible-srpm-macros-1-16.1.el10_0.noarch.rpm [Connection timed out after 30001 milliseconds] [MIRROR] epel-rpm-macros-10-6.el10_2.noarch.rpm: Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/epel/10.2/Everything/ppc64le/Packages/e/epel-rpm-macros-10-6.el10_2.noarch.rpm [Connection timed out after 30001 milliseconds] (145/148): epel-rpm-macros-10-6.el10_2.noarch.r 279 B/s | 8.2 kB 00:30 (146/148): ansible-srpm-macros-1-16.1.el10_0.no 679 B/s | 20 kB 00:30 (147/148): ghc-srpm-macros-1.9.2-1.el10_0.noarc 122 kB/s | 9.1 kB 00:00 [MIRROR] fpc-srpm-macros-1.3-7.el10_1.noarch.rpm: Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/epel/10.2/Everything/ppc64le/Packages/f/fpc-srpm-macros-1.3-7.el10_1.noarch.rpm [Connection timed out after 30001 milliseconds] (148/148): fpc-srpm-macros-1.3-7.el10_1.noarch. 266 B/s | 7.8 kB 00:30 -------------------------------------------------------------------------------- Total 1.1 MB/s | 64 MB 00:55 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 - ppc64l 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.ppc64le 1/1 Preparing : 1/1 Installing : libgcc-14.3.1-4.2.el10.ppc64le 1/148 Running scriptlet: libgcc-14.3.1-4.2.el10.ppc64le 1/148 Installing : ghc-srpm-macros-1.9.2-1.el10_0.noarch 2/148 Installing : fpc-srpm-macros-1.3-7.el10_1.noarch 3/148 Installing : ansible-srpm-macros-1-16.1.el10_0.noarch 4/148 Installing : rust-toolset-srpm-macros-1.92.0-1.el10.noarch 5/148 Installing : qt6-srpm-macros-6.10.1-1.el10.noarch 6/148 Installing : perl-srpm-macros-1-57.el10.noarch 7/148 Installing : package-notes-srpm-macros-0.5-13.el10.noarch 8/148 Installing : openblas-srpm-macros-2-19.el10.noarch 9/148 Installing : ocaml-srpm-macros-10-4.el10.noarch 10/148 Installing : kernel-srpm-macros-1.0-27.el10.noarch 11/148 Installing : publicsuffix-list-dafsa-20240107-5.el10.noarch 12/148 Installing : pkgconf-m4-2.1.0-3.el10.noarch 13/148 Installing : pcre2-syntax-10.44-1.el10.3.noarch 14/148 Installing : ncurses-base-6.4-14.20240127.el10.noarch 15/148 Installing : libssh-config-0.11.1-3.el10.noarch 16/148 Installing : coreutils-common-9.5-6.el10.ppc64le 17/148 Installing : centos-gpg-keys-10.0-19.el10.noarch 18/148 Installing : centos-stream-repos-10.0-19.el10.noarch 19/148 Installing : centos-stream-release-10.0-19.el10.noarch 20/148 Installing : setup-2.14.5-7.el10.noarch 21/148 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.5-7.el10.noarch 21/148 Installing : filesystem-3.18-17.el10.ppc64le 22/148 Installing : basesystem-11-22.el10.noarch 23/148 Installing : glibc-gconv-extra-2.39-99.el10.ppc64le 24/148 Running scriptlet: glibc-gconv-extra-2.39-99.el10.ppc64le 24/148 Installing : glibc-minimal-langpack-2.39-99.el10.ppc64le 25/148 Installing : glibc-common-2.39-99.el10.ppc64le 26/148 Running scriptlet: glibc-2.39-99.el10.ppc64le 27/148 Installing : glibc-2.39-99.el10.ppc64le 27/148 Running scriptlet: glibc-2.39-99.el10.ppc64le 27/148 Installing : ncurses-libs-6.4-14.20240127.el10.ppc64le 28/148 Installing : bash-5.2.26-6.el10.ppc64le 29/148 Running scriptlet: bash-5.2.26-6.el10.ppc64le 29/148 Installing : zlib-ng-compat-2.2.3-3.el10.ppc64le 30/148 Installing : bzip2-libs-1.0.8-25.el10.ppc64le 31/148 Installing : xz-libs-1:5.6.2-4.el10.ppc64le 32/148 Installing : readline-8.2-11.el10.ppc64le 33/148 Installing : libstdc++-14.3.1-4.2.el10.ppc64le 34/148 Installing : libuuid-2.40.2-13.el10.ppc64le 35/148 Installing : popt-1.19-8.el10.ppc64le 36/148 Installing : libblkid-2.40.2-13.el10.ppc64le 37/148 Installing : gmp-1:6.2.1-12.el10.ppc64le 38/148 Installing : libattr-2.5.2-5.el10.ppc64le 39/148 Installing : libacl-2.3.2-4.el10.ppc64le 40/148 Installing : libxcrypt-4.4.36-10.el10.ppc64le 41/148 Installing : libzstd-1.5.5-9.el10.ppc64le 42/148 Installing : elfutils-libelf-0.194-1.el10.ppc64le 43/148 Running scriptlet: crypto-policies-20251127-1.git27c2902.el10.noarc 44/148 Installing : crypto-policies-20251127-1.git27c2902.el10.noarc 44/148 Running scriptlet: crypto-policies-20251127-1.git27c2902.el10.noarc 44/148 Installing : gdbm-libs-1:1.23-14.el10.ppc64le 45/148 Installing : libeconf-0.6.2-4.el10.ppc64le 46/148 Installing : dwz-0.16-1.el10.ppc64le 47/148 Installing : mpfr-4.2.1-6.el10.ppc64le 48/148 Installing : gawk-5.3.0-6.el10.ppc64le 49/148 Installing : unzip-6.0-69.el10.ppc64le 50/148 Installing : file-libs-5.45-8.el10.ppc64le 51/148 Installing : file-5.45-8.el10.ppc64le 52/148 Installing : alternatives-1.30-2.el10.ppc64le 53/148 Installing : jansson-2.14-3.el10.ppc64le 54/148 Installing : libcap-ng-0.8.4-6.el10.ppc64le 55/148 Installing : audit-libs-4.0.3-5.el10.ppc64le 56/148 Installing : pam-libs-1.6.1-9.el10.ppc64le 57/148 Installing : libcap-2.69-7.el10.ppc64le 58/148 Installing : systemd-libs-257-21.el10.ppc64le 59/148 Installing : libffi-3.4.4-10.el10.ppc64le 60/148 Installing : libsepol-3.9-1.el10.ppc64le 61/148 Installing : libsmartcols-2.40.2-13.el10.ppc64le 62/148 Installing : libtasn1-4.20.0-1.el10.ppc64le 63/148 Installing : libunistring-1.1-10.el10.ppc64le 64/148 Installing : libidn2-2.3.7-3.el10.ppc64le 65/148 Installing : lua-libs-5.4.6-7.el10.ppc64le 66/148 Installing : lz4-libs-1.9.4-8.el10.ppc64le 67/148 Installing : pcre2-10.44-1.el10.3.ppc64le 68/148 Installing : libselinux-3.9-3.el10.ppc64le 69/148 Installing : sed-4.9-3.el10.ppc64le 70/148 Installing : findutils-1:4.10.0-5.el10.ppc64le 71/148 Installing : grep-3.11-10.el10.ppc64le 72/148 Installing : xz-1:5.6.2-4.el10.ppc64le 73/148 Installing : libmount-2.40.2-13.el10.ppc64le 74/148 Installing : util-linux-core-2.40.2-13.el10.ppc64le 75/148 Installing : libsemanage-3.9-2.el10.ppc64le 76/148 Installing : shadow-utils-2:4.15.0-9.el10.ppc64le 77/148 Running scriptlet: libutempter-1.2.1-15.el10.ppc64le 78/148 Installing : libutempter-1.2.1-15.el10.ppc64le 78/148 Installing : tar-2:1.35-10.el10.ppc64le 79/148 Installing : zstd-1.5.5-9.el10.ppc64le 80/148 Installing : libpsl-0.21.5-6.el10.ppc64le 81/148 Installing : p11-kit-0.26.1-1.el10.ppc64le 82/148 Installing : p11-kit-trust-0.26.1-1.el10.ppc64le 83/148 Running scriptlet: p11-kit-trust-0.26.1-1.el10.ppc64le 83/148 Installing : openssl-fips-provider-1:3.5.1-6.el10.ppc64le 84/148 Installing : openssl-libs-1:3.5.1-6.el10.ppc64le 85/148 Installing : coreutils-9.5-6.el10.ppc64le 86/148 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar 87/148 Installing : ca-certificates-2025.2.80_v9.0.305-102.el10.noar 87/148 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar 87/148 Installing : authselect-libs-1.5.0-8.el10.ppc64le 88/148 Installing : gzip-1.13-3.el10.ppc64le 89/148 Installing : cracklib-2.9.11-8.el10.ppc64le 90/148 Installing : cracklib-dicts-2.9.11-8.el10.ppc64le 91/148 Installing : libpwquality-1.4.5-12.el10.ppc64le 92/148 Installing : libevent-2.1.12-16.el10.ppc64le 93/148 Installing : rpm-sequoia-1.9.0.3-1.el10.ppc64le 94/148 Installing : zip-3.0-45.el10.ppc64le 95/148 Installing : cyrus-sasl-lib-2.1.28-27.el10.ppc64le 96/148 Installing : openldap-2.6.10-1.el10.ppc64le 97/148 Installing : gdbm-1:1.23-14.el10.ppc64le 98/148 Installing : pam-1.6.1-9.el10.ppc64le 99/148 Installing : libfdisk-2.40.2-13.el10.ppc64le 100/148 Installing : libxml2-2.12.5-9.el10.ppc64le 101/148 Installing : libarchive-3.7.7-4.el10.ppc64le 102/148 Installing : bzip2-1.0.8-25.el10.ppc64le 103/148 Installing : sqlite-libs-3.46.1-5.el10.ppc64le 104/148 Installing : rpm-libs-4.19.1.1-21.el10.ppc64le 105/148 Installing : ed-1.20-5.el10.ppc64le 106/148 Installing : patch-2.7.6-26.el10.ppc64le 107/148 Installing : elfutils-default-yama-scope-0.194-1.el10.noarch 108/148 Running scriptlet: elfutils-default-yama-scope-0.194-1.el10.noarch 108/148 Installing : cpio-2.15-3.el10.ppc64le 109/148 Installing : diffutils-3.10-8.el10.ppc64le 110/148 Installing : json-c-0.18-3.el10.ppc64le 111/148 Installing : keyutils-libs-1.6.3-5.el10.ppc64le 112/148 Installing : libbrotli-1.1.0-7.el10.ppc64le 113/148 Installing : libcom_err-1.47.1-5.el10.ppc64le 114/148 Installing : libgomp-14.3.1-4.2.el10.ppc64le 115/148 Installing : libnghttp2-1.64.0-2.el10.ppc64le 116/148 Installing : libpkgconf-2.1.0-3.el10.ppc64le 117/148 Installing : pkgconf-2.1.0-3.el10.ppc64le 118/148 Installing : pkgconf-pkg-config-2.1.0-3.el10.ppc64le 119/148 Installing : librtas-2.0.6-4.el10.ppc64le 120/148 Running scriptlet: librtas-2.0.6-4.el10.ppc64le 120/148 Installing : libverto-0.3.2-10.el10.ppc64le 121/148 Installing : krb5-libs-1.21.3-8.el10.ppc64le 122/148 Installing : libssh-0.11.1-3.el10.ppc64le 123/148 Installing : libcurl-8.12.1-4.el10.ppc64le 124/148 Installing : elfutils-libs-0.194-1.el10.ppc64le 125/148 Installing : elfutils-debuginfod-client-0.194-1.el10.ppc64le 126/148 Installing : binutils-gold-2.41-60.el10.ppc64le 127/148 Running scriptlet: binutils-gold-2.41-60.el10.ppc64le 127/148 Installing : binutils-2.41-60.el10.ppc64le 128/148 Running scriptlet: binutils-2.41-60.el10.ppc64le 128/148 Installing : elfutils-0.194-1.el10.ppc64le 129/148 Installing : gdb-minimal-16.3-2.el10.ppc64le 130/148 Installing : debugedit-5.1-8.el10.ppc64le 131/148 Installing : rpm-build-libs-4.19.1.1-21.el10.ppc64le 132/148 Installing : curl-8.12.1-4.el10.ppc64le 133/148 Running scriptlet: rpm-4.19.1.1-21.el10.ppc64le 134/148 Installing : rpm-4.19.1.1-21.el10.ppc64le 134/148 Installing : efi-srpm-macros-6-6.el10.noarch 135/148 Installing : lua-srpm-macros-1-15.el10.noarch 136/148 Installing : fonts-srpm-macros-1:2.0.5-18.el10.noarch 137/148 Installing : forge-srpm-macros-0.4.0-6.el10.noarch 138/148 Installing : go-srpm-macros-3.8.0-1.el10.noarch 139/148 Installing : python-srpm-macros-3.12-11.el10.noarch 140/148 Installing : redhat-rpm-config-295-1.el10.noarch 141/148 Installing : rpm-build-4.19.1.1-21.el10.ppc64le 142/148 Installing : pyproject-srpm-macros-1.18.5-1.el10.noarch 143/148 Installing : util-linux-2.40.2-13.el10.ppc64le 144/148 Running scriptlet: util-linux-2.40.2-13.el10.ppc64le 144/148 Installing : authselect-1.5.0-8.el10.ppc64le 145/148 Installing : which-2.21-44.el10.ppc64le 146/148 Installing : info-7.1-6.el10.ppc64le 147/148 Installing : epel-rpm-macros-10-6.el10_2.noarch 148/148 Running scriptlet: filesystem-3.18-17.el10.ppc64le 148/148 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar 148/148 Running scriptlet: authselect-libs-1.5.0-8.el10.ppc64le 148/148 Running scriptlet: rpm-4.19.1.1-21.el10.ppc64le 148/148 Running scriptlet: epel-rpm-macros-10-6.el10_2.noarch 148/148 Installed: alternatives-1.30-2.el10.ppc64le ansible-srpm-macros-1-16.1.el10_0.noarch audit-libs-4.0.3-5.el10.ppc64le authselect-1.5.0-8.el10.ppc64le authselect-libs-1.5.0-8.el10.ppc64le basesystem-11-22.el10.noarch bash-5.2.26-6.el10.ppc64le binutils-2.41-60.el10.ppc64le binutils-gold-2.41-60.el10.ppc64le bzip2-1.0.8-25.el10.ppc64le bzip2-libs-1.0.8-25.el10.ppc64le 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.ppc64le coreutils-common-9.5-6.el10.ppc64le cpio-2.15-3.el10.ppc64le cracklib-2.9.11-8.el10.ppc64le cracklib-dicts-2.9.11-8.el10.ppc64le crypto-policies-20251127-1.git27c2902.el10.noarch curl-8.12.1-4.el10.ppc64le cyrus-sasl-lib-2.1.28-27.el10.ppc64le debugedit-5.1-8.el10.ppc64le diffutils-3.10-8.el10.ppc64le dwz-0.16-1.el10.ppc64le ed-1.20-5.el10.ppc64le efi-srpm-macros-6-6.el10.noarch elfutils-0.194-1.el10.ppc64le elfutils-debuginfod-client-0.194-1.el10.ppc64le elfutils-default-yama-scope-0.194-1.el10.noarch elfutils-libelf-0.194-1.el10.ppc64le elfutils-libs-0.194-1.el10.ppc64le epel-rpm-macros-10-6.el10_2.noarch file-5.45-8.el10.ppc64le file-libs-5.45-8.el10.ppc64le filesystem-3.18-17.el10.ppc64le findutils-1:4.10.0-5.el10.ppc64le 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.ppc64le gdb-minimal-16.3-2.el10.ppc64le gdbm-1:1.23-14.el10.ppc64le gdbm-libs-1:1.23-14.el10.ppc64le ghc-srpm-macros-1.9.2-1.el10_0.noarch glibc-2.39-99.el10.ppc64le glibc-common-2.39-99.el10.ppc64le glibc-gconv-extra-2.39-99.el10.ppc64le glibc-minimal-langpack-2.39-99.el10.ppc64le gmp-1:6.2.1-12.el10.ppc64le go-srpm-macros-3.8.0-1.el10.noarch grep-3.11-10.el10.ppc64le gzip-1.13-3.el10.ppc64le info-7.1-6.el10.ppc64le jansson-2.14-3.el10.ppc64le json-c-0.18-3.el10.ppc64le kernel-srpm-macros-1.0-27.el10.noarch keyutils-libs-1.6.3-5.el10.ppc64le krb5-libs-1.21.3-8.el10.ppc64le libacl-2.3.2-4.el10.ppc64le libarchive-3.7.7-4.el10.ppc64le libattr-2.5.2-5.el10.ppc64le libblkid-2.40.2-13.el10.ppc64le libbrotli-1.1.0-7.el10.ppc64le libcap-2.69-7.el10.ppc64le libcap-ng-0.8.4-6.el10.ppc64le libcom_err-1.47.1-5.el10.ppc64le libcurl-8.12.1-4.el10.ppc64le libeconf-0.6.2-4.el10.ppc64le libevent-2.1.12-16.el10.ppc64le libfdisk-2.40.2-13.el10.ppc64le libffi-3.4.4-10.el10.ppc64le libgcc-14.3.1-4.2.el10.ppc64le libgomp-14.3.1-4.2.el10.ppc64le libidn2-2.3.7-3.el10.ppc64le libmount-2.40.2-13.el10.ppc64le libnghttp2-1.64.0-2.el10.ppc64le libpkgconf-2.1.0-3.el10.ppc64le libpsl-0.21.5-6.el10.ppc64le libpwquality-1.4.5-12.el10.ppc64le librtas-2.0.6-4.el10.ppc64le libselinux-3.9-3.el10.ppc64le libsemanage-3.9-2.el10.ppc64le libsepol-3.9-1.el10.ppc64le libsmartcols-2.40.2-13.el10.ppc64le libssh-0.11.1-3.el10.ppc64le libssh-config-0.11.1-3.el10.noarch libstdc++-14.3.1-4.2.el10.ppc64le libtasn1-4.20.0-1.el10.ppc64le libunistring-1.1-10.el10.ppc64le libutempter-1.2.1-15.el10.ppc64le libuuid-2.40.2-13.el10.ppc64le libverto-0.3.2-10.el10.ppc64le libxcrypt-4.4.36-10.el10.ppc64le libxml2-2.12.5-9.el10.ppc64le libzstd-1.5.5-9.el10.ppc64le lua-libs-5.4.6-7.el10.ppc64le lua-srpm-macros-1-15.el10.noarch lz4-libs-1.9.4-8.el10.ppc64le mpfr-4.2.1-6.el10.ppc64le ncurses-base-6.4-14.20240127.el10.noarch ncurses-libs-6.4-14.20240127.el10.ppc64le ocaml-srpm-macros-10-4.el10.noarch openblas-srpm-macros-2-19.el10.noarch openldap-2.6.10-1.el10.ppc64le openssl-fips-provider-1:3.5.1-6.el10.ppc64le openssl-libs-1:3.5.1-6.el10.ppc64le p11-kit-0.26.1-1.el10.ppc64le p11-kit-trust-0.26.1-1.el10.ppc64le package-notes-srpm-macros-0.5-13.el10.noarch pam-1.6.1-9.el10.ppc64le pam-libs-1.6.1-9.el10.ppc64le patch-2.7.6-26.el10.ppc64le pcre2-10.44-1.el10.3.ppc64le pcre2-syntax-10.44-1.el10.3.noarch perl-srpm-macros-1-57.el10.noarch pkgconf-2.1.0-3.el10.ppc64le pkgconf-m4-2.1.0-3.el10.noarch pkgconf-pkg-config-2.1.0-3.el10.ppc64le popt-1.19-8.el10.ppc64le 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.ppc64le redhat-rpm-config-295-1.el10.noarch rpm-4.19.1.1-21.el10.ppc64le rpm-build-4.19.1.1-21.el10.ppc64le rpm-build-libs-4.19.1.1-21.el10.ppc64le rpm-libs-4.19.1.1-21.el10.ppc64le rpm-sequoia-1.9.0.3-1.el10.ppc64le rust-toolset-srpm-macros-1.92.0-1.el10.noarch sed-4.9-3.el10.ppc64le setup-2.14.5-7.el10.noarch shadow-utils-2:4.15.0-9.el10.ppc64le sqlite-libs-3.46.1-5.el10.ppc64le systemd-libs-257-21.el10.ppc64le tar-2:1.35-10.el10.ppc64le unzip-6.0-69.el10.ppc64le util-linux-2.40.2-13.el10.ppc64le util-linux-core-2.40.2-13.el10.ppc64le which-2.21-44.el10.ppc64le xz-1:5.6.2-4.el10.ppc64le xz-libs-1:5.6.2-4.el10.ppc64le zip-3.0-45.el10.ppc64le zlib-ng-compat-2.2.3-3.el10.ppc64le zstd-1.5.5-9.el10.ppc64le 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.ppc64le ansible-srpm-macros-1-16.1.el10_0.noarch audit-libs-4.0.3-5.el10.ppc64le authselect-1.5.0-8.el10.ppc64le authselect-libs-1.5.0-8.el10.ppc64le basesystem-11-22.el10.noarch bash-5.2.26-6.el10.ppc64le binutils-2.41-60.el10.ppc64le binutils-gold-2.41-60.el10.ppc64le bzip2-1.0.8-25.el10.ppc64le bzip2-libs-1.0.8-25.el10.ppc64le 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.ppc64le coreutils-common-9.5-6.el10.ppc64le cpio-2.15-3.el10.ppc64le cracklib-2.9.11-8.el10.ppc64le cracklib-dicts-2.9.11-8.el10.ppc64le crypto-policies-20251127-1.git27c2902.el10.noarch curl-8.12.1-4.el10.ppc64le cyrus-sasl-lib-2.1.28-27.el10.ppc64le debugedit-5.1-8.el10.ppc64le diffutils-3.10-8.el10.ppc64le dwz-0.16-1.el10.ppc64le ed-1.20-5.el10.ppc64le efi-srpm-macros-6-6.el10.noarch elfutils-0.194-1.el10.ppc64le elfutils-debuginfod-client-0.194-1.el10.ppc64le elfutils-default-yama-scope-0.194-1.el10.noarch elfutils-libelf-0.194-1.el10.ppc64le elfutils-libs-0.194-1.el10.ppc64le epel-rpm-macros-10-6.el10_2.noarch file-5.45-8.el10.ppc64le file-libs-5.45-8.el10.ppc64le filesystem-3.18-17.el10.ppc64le findutils-4.10.0-5.el10.ppc64le 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.ppc64le gdb-minimal-16.3-2.el10.ppc64le gdbm-1.23-14.el10.ppc64le gdbm-libs-1.23-14.el10.ppc64le ghc-srpm-macros-1.9.2-1.el10_0.noarch glibc-2.39-99.el10.ppc64le glibc-common-2.39-99.el10.ppc64le glibc-gconv-extra-2.39-99.el10.ppc64le glibc-minimal-langpack-2.39-99.el10.ppc64le gmp-6.2.1-12.el10.ppc64le go-srpm-macros-3.8.0-1.el10.noarch gpg-pubkey-8483c65d-5ccc5b19 gpg-pubkey-e37ed158-65785fa9 grep-3.11-10.el10.ppc64le gzip-1.13-3.el10.ppc64le info-7.1-6.el10.ppc64le jansson-2.14-3.el10.ppc64le json-c-0.18-3.el10.ppc64le kernel-srpm-macros-1.0-27.el10.noarch keyutils-libs-1.6.3-5.el10.ppc64le krb5-libs-1.21.3-8.el10.ppc64le libacl-2.3.2-4.el10.ppc64le libarchive-3.7.7-4.el10.ppc64le libattr-2.5.2-5.el10.ppc64le libblkid-2.40.2-13.el10.ppc64le libbrotli-1.1.0-7.el10.ppc64le libcap-2.69-7.el10.ppc64le libcap-ng-0.8.4-6.el10.ppc64le libcom_err-1.47.1-5.el10.ppc64le libcurl-8.12.1-4.el10.ppc64le libeconf-0.6.2-4.el10.ppc64le libevent-2.1.12-16.el10.ppc64le libfdisk-2.40.2-13.el10.ppc64le libffi-3.4.4-10.el10.ppc64le libgcc-14.3.1-4.2.el10.ppc64le libgomp-14.3.1-4.2.el10.ppc64le libidn2-2.3.7-3.el10.ppc64le libmount-2.40.2-13.el10.ppc64le libnghttp2-1.64.0-2.el10.ppc64le libpkgconf-2.1.0-3.el10.ppc64le libpsl-0.21.5-6.el10.ppc64le libpwquality-1.4.5-12.el10.ppc64le librtas-2.0.6-4.el10.ppc64le libselinux-3.9-3.el10.ppc64le libsemanage-3.9-2.el10.ppc64le libsepol-3.9-1.el10.ppc64le libsmartcols-2.40.2-13.el10.ppc64le libssh-0.11.1-3.el10.ppc64le libssh-config-0.11.1-3.el10.noarch libstdc++-14.3.1-4.2.el10.ppc64le libtasn1-4.20.0-1.el10.ppc64le libunistring-1.1-10.el10.ppc64le libutempter-1.2.1-15.el10.ppc64le libuuid-2.40.2-13.el10.ppc64le libverto-0.3.2-10.el10.ppc64le libxcrypt-4.4.36-10.el10.ppc64le libxml2-2.12.5-9.el10.ppc64le libzstd-1.5.5-9.el10.ppc64le lua-libs-5.4.6-7.el10.ppc64le lua-srpm-macros-1-15.el10.noarch lz4-libs-1.9.4-8.el10.ppc64le mpfr-4.2.1-6.el10.ppc64le ncurses-base-6.4-14.20240127.el10.noarch ncurses-libs-6.4-14.20240127.el10.ppc64le ocaml-srpm-macros-10-4.el10.noarch openblas-srpm-macros-2-19.el10.noarch openldap-2.6.10-1.el10.ppc64le openssl-fips-provider-3.5.1-6.el10.ppc64le openssl-libs-3.5.1-6.el10.ppc64le p11-kit-0.26.1-1.el10.ppc64le p11-kit-trust-0.26.1-1.el10.ppc64le package-notes-srpm-macros-0.5-13.el10.noarch pam-1.6.1-9.el10.ppc64le pam-libs-1.6.1-9.el10.ppc64le patch-2.7.6-26.el10.ppc64le pcre2-10.44-1.el10.3.ppc64le pcre2-syntax-10.44-1.el10.3.noarch perl-srpm-macros-1-57.el10.noarch pkgconf-2.1.0-3.el10.ppc64le pkgconf-m4-2.1.0-3.el10.noarch pkgconf-pkg-config-2.1.0-3.el10.ppc64le popt-1.19-8.el10.ppc64le 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.ppc64le redhat-rpm-config-295-1.el10.noarch rpm-4.19.1.1-21.el10.ppc64le rpm-build-4.19.1.1-21.el10.ppc64le rpm-build-libs-4.19.1.1-21.el10.ppc64le rpm-libs-4.19.1.1-21.el10.ppc64le rpm-sequoia-1.9.0.3-1.el10.ppc64le rust-toolset-srpm-macros-1.92.0-1.el10.noarch sed-4.9-3.el10.ppc64le setup-2.14.5-7.el10.noarch shadow-utils-4.15.0-9.el10.ppc64le sqlite-libs-3.46.1-5.el10.ppc64le systemd-libs-257-21.el10.ppc64le tar-1.35-10.el10.ppc64le unzip-6.0-69.el10.ppc64le util-linux-2.40.2-13.el10.ppc64le util-linux-core-2.40.2-13.el10.ppc64le which-2.21-44.el10.ppc64le xz-5.6.2-4.el10.ppc64le xz-libs-5.6.2-4.el10.ppc64le zip-3.0-45.el10.ppc64le zlib-ng-compat-2.2.3-3.el10.ppc64le zstd-1.5.5-9.el10.ppc64le Start: buildsrpm Start: rpmbuild -bs Building target platforms: ppc64le Building for target ppc64le 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-ppc64le-1769509936.247694/root/var/log/dnf.rpm.log /var/lib/mock/centos-stream+epel-10-ppc64le-1769509936.247694/root/var/log/dnf.librepo.log /var/lib/mock/centos-stream+epel-10-ppc64le-1769509936.247694/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-g0nsw1_5/samtools/samtools.spec) Config(child) 2 minutes 59 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-ppc64le) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-ppc64le-bootstrap-1769509936.247694/root. INFO: reusing tmpfs at /var/lib/mock/centos-stream+epel-10-ppc64le-bootstrap-1769509936.247694/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-ppc64le-1769509936.247694/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.ppc64le rpm-sequoia-1.9.0.3-1.el10.ppc64le 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: ppc64le Building for target ppc64le 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 1.2 kB/s | 1.5 kB 00:01 CentOS Stream 10 - BaseOS 242 kB/s | 22 kB 00:00 CentOS Stream 10 - AppStream 693 kB/s | 22 kB 00:00 CentOS Stream 10 - CRB 575 kB/s | 20 kB 00:00 CentOS Stream 10 - Extras packages 835 kB/s | 28 kB 00:00 Extra Packages for Enterprise Linux 10 - ppc64l 689 kB/s | 27 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: gcc ppc64le 14.3.1-4.2.el10 appstream 33 M htslib-devel ppc64le 1.23-1.el10 copr_base 107 k htslib-tools ppc64le 1.23-1.el10 copr_base 806 k make ppc64le 1:4.4.1-9.el10 baseos 600 k ncurses-devel ppc64le 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 ppc64le 4:5.40.2-514.el10 appstream 73 k perl-lib ppc64le 0.65-514.el10 appstream 16 k zlib-ng-compat-devel ppc64le 2.2.3-3.el10 appstream 36 k Installing dependencies: annobin-docs noarch 13.02-2.el10 appstream 87 k annobin-plugin-gcc ppc64le 13.02-2.el10 appstream 998 k cmake-filesystem ppc64le 3.31.8-1.el10 appstream 21 k cpp ppc64le 14.3.1-4.2.el10 appstream 11 M gcc-plugin-annobin ppc64le 14.3.1-4.2.el10 appstream 71 k glibc-devel ppc64le 2.39-99.el10 appstream 599 k groff-base ppc64le 1.23.0-10.el10 baseos 1.1 M htslib ppc64le 1.23-1.el10 copr_base 634 k kernel-headers ppc64le 6.12.0-191.el10 appstream 3.1 M libasan ppc64le 14.3.1-4.2.el10 appstream 540 k libatomic ppc64le 14.3.1-4.2.el10 baseos 56 k libmpc ppc64le 1.3.1-7.el10 appstream 77 k libubsan ppc64le 14.3.1-4.2.el10 appstream 262 k libxcrypt-devel ppc64le 4.4.36-10.el10 appstream 30 k ncurses ppc64le 6.4-14.20240127.el10 baseos 431 k ncurses-c++-libs ppc64le 6.4-14.20240127.el10 appstream 40 k perl-AutoLoader noarch 5.74-514.el10 appstream 22 k perl-B ppc64le 1.89-514.el10 appstream 181 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 ppc64le 2.189-512.el10 baseos 58 k perl-Digest noarch 1.20-511.el10 baseos 26 k perl-Digest-MD5 ppc64le 2.59-6.el10 baseos 37 k perl-DynaLoader ppc64le 1.56-514.el10 appstream 27 k perl-Encode ppc64le 4:3.21-511.el10 baseos 1.1 M perl-Errno ppc64le 1.38-514.el10 appstream 16 k perl-Exporter noarch 5.78-511.el10 baseos 32 k perl-Fcntl ppc64le 1.18-514.el10 appstream 31 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 ppc64le 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 ppc64le 3.16-511.el10 baseos 32 k perl-Mozilla-CA noarch 20231213-5.el10 baseos 15 k perl-Net-SSLeay ppc64le 1.94-8.el10 appstream 394 k perl-POSIX ppc64le 2.20-514.el10 appstream 99 k perl-PathTools ppc64le 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 ppc64le 5:1.63-511.el10 baseos 77 k perl-SelectSaver noarch 1.02-514.el10 appstream 12 k perl-Socket ppc64le 4:2.038-511.el10 baseos 56 k perl-Storable ppc64le 1:3.32-511.el10 baseos 103 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 ppc64le 4:5.40.2-514.el10 appstream 2.5 M perl-locale noarch 1.12-514.el10 appstream 14 k perl-mro ppc64le 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 81 Packages Total download size: 61 M Installed size: 179 M Downloading Packages: (1/81): htslib-devel-1.23-1.el10.ppc64le.rpm 453 kB/s | 107 kB 00:00 (2/81): htslib-tools-1.23-1.el10.ppc64le.rpm 2.6 MB/s | 806 kB 00:00 (3/81): htslib-1.23-1.el10.ppc64le.rpm 1.9 MB/s | 634 kB 00:00 (4/81): libatomic-14.3.1-4.2.el10.ppc64le.rpm 86 kB/s | 56 kB 00:00 (5/81): make-4.4.1-9.el10.ppc64le.rpm 562 kB/s | 600 kB 00:01 (6/81): groff-base-1.23.0-10.el10.ppc64le.rpm 897 kB/s | 1.1 MB 00:01 (7/81): perl-Carp-1.54-511.el10.noarch.rpm 204 kB/s | 30 kB 00:00 (8/81): ncurses-6.4-14.20240127.el10.ppc64le.rp 712 kB/s | 431 kB 00:00 (9/81): perl-Digest-1.20-511.el10.noarch.rpm 171 kB/s | 26 kB 00:00 (10/81): perl-Data-Dumper-2.189-512.el10.ppc64l 348 kB/s | 58 kB 00:00 (11/81): perl-Digest-MD5-2.59-6.el10.ppc64le.rp 220 kB/s | 37 kB 00:00 (12/81): perl-Exporter-5.78-511.el10.noarch.rpm 237 kB/s | 32 kB 00:00 (13/81): perl-File-Temp-0.231.100-512.el10.noar 322 kB/s | 60 kB 00:00 (14/81): perl-Getopt-Long-2.58-3.el10.noarch.rp 432 kB/s | 65 kB 00:00 (15/81): perl-Encode-3.21-511.el10.ppc64le.rpm 3.1 MB/s | 1.1 MB 00:00 (16/81): perl-HTTP-Tiny-0.088-512.el10.noarch.r 395 kB/s | 57 kB 00:00 (17/81): perl-IO-Socket-IP-0.42-512.el10.noarch 323 kB/s | 43 kB 00:00 (18/81): perl-IO-Socket-SSL-2.085-3.el10.noarch 1.3 MB/s | 227 kB 00:00 (19/81): perl-MIME-Base64-3.16-511.el10.ppc64le 187 kB/s | 32 kB 00:00 (20/81): perl-Mozilla-CA-20231213-5.el10.noarch 101 kB/s | 15 kB 00:00 (21/81): perl-Pod-Escapes-1.07-511.el10.noarch. 153 kB/s | 21 kB 00:00 (22/81): perl-PathTools-3.91-512.el10.ppc64le.r 496 kB/s | 85 kB 00:00 (23/81): perl-Pod-Perldoc-3.28.01-512.el10.noar 596 kB/s | 84 kB 00:00 (24/81): perl-Scalar-List-Utils-1.63-511.el10.p 475 kB/s | 77 kB 00:00 (25/81): perl-Pod-Usage-2.03-511.el10.noarch.rp 205 kB/s | 41 kB 00:00 (26/81): perl-Pod-Simple-3.45-511.el10.noarch.r 834 kB/s | 218 kB 00:00 (27/81): perl-Socket-2.038-511.el10.ppc64le.rpm 423 kB/s | 56 kB 00:00 (28/81): perl-Storable-3.32-511.el10.ppc64le.rp 611 kB/s | 103 kB 00:00 (29/81): perl-Term-ANSIColor-5.01-512.el10.noar 317 kB/s | 49 kB 00:00 (30/81): perl-Term-Cap-1.18-511.el10.noarch.rpm 171 kB/s | 23 kB 00:00 (31/81): perl-Text-ParseWords-3.31-511.el10.noa 104 kB/s | 17 kB 00:00 (32/81): perl-Text-Tabs+Wrap-2024.001-511.el10. 160 kB/s | 23 kB 00:00 (33/81): perl-Time-Local-1.350-511.el10.noarch. 226 kB/s | 35 kB 00:00 (34/81): perl-URI-5.27-3.el10.noarch.rpm 853 kB/s | 134 kB 00:00 (35/81): perl-constant-1.33-512.el10.noarch.rpm 163 kB/s | 24 kB 00:00 (36/81): perl-libnet-3.15-512.el10.noarch.rpm 646 kB/s | 127 kB 00:00 (37/81): perl-parent-0.241-512.el10.noarch.rpm 115 kB/s | 16 kB 00:00 (38/81): perl-podlators-5.01-511.el10.noarch.rp 740 kB/s | 124 kB 00:00 (39/81): cmake-filesystem-3.31.8-1.el10.ppc64le 294 kB/s | 21 kB 00:00 (40/81): annobin-docs-13.02-2.el10.noarch.rpm 621 kB/s | 87 kB 00:00 (41/81): annobin-plugin-gcc-13.02-2.el10.ppc64l 4.8 MB/s | 998 kB 00:00 (42/81): gcc-plugin-annobin-14.3.1-4.2.el10.ppc 3.0 MB/s | 71 kB 00:00 (43/81): glibc-devel-2.39-99.el10.ppc64le.rpm 16 MB/s | 599 kB 00:00 (44/81): kernel-headers-6.12.0-191.el10.ppc64le 31 MB/s | 3.1 MB 00:00 (45/81): cpp-14.3.1-4.2.el10.ppc64le.rpm 33 MB/s | 11 MB 00:00 (46/81): libasan-14.3.1-4.2.el10.ppc64le.rpm 7.0 MB/s | 540 kB 00:00 (47/81): libmpc-1.3.1-7.el10.ppc64le.rpm 3.1 MB/s | 77 kB 00:00 (48/81): libubsan-14.3.1-4.2.el10.ppc64le.rpm 9.5 MB/s | 262 kB 00:00 (49/81): libxcrypt-devel-4.4.36-10.el10.ppc64le 1.3 MB/s | 30 kB 00:00 (50/81): gcc-14.3.1-4.2.el10.ppc64le.rpm 60 MB/s | 33 MB 00:00 (51/81): ncurses-c++-libs-6.4-14.20240127.el10. 199 kB/s | 40 kB 00:00 (52/81): ncurses-devel-6.4-14.20240127.el10.ppc 3.9 MB/s | 753 kB 00:00 (53/81): perl-AutoLoader-5.74-514.el10.noarch.r 839 kB/s | 22 kB 00:00 (54/81): perl-B-1.89-514.el10.ppc64le.rpm 6.4 MB/s | 181 kB 00:00 (55/81): perl-Class-Struct-0.68-514.el10.noarch 949 kB/s | 23 kB 00:00 (56/81): perl-DynaLoader-1.56-514.el10.ppc64le. 1.0 MB/s | 27 kB 00:00 (57/81): perl-Errno-1.38-514.el10.ppc64le.rpm 658 kB/s | 16 kB 00:00 (58/81): perl-Fcntl-1.18-514.el10.ppc64le.rpm 1.2 MB/s | 31 kB 00:00 (59/81): perl-File-Path-2.18-512.el10.noarch.rp 1.4 MB/s | 35 kB 00:00 (60/81): perl-File-Basename-2.86-514.el10.noarc 698 kB/s | 18 kB 00:00 (61/81): perl-File-stat-1.14-514.el10.noarch.rp 707 kB/s | 18 kB 00:00 (62/81): perl-FileHandle-2.05-514.el10.noarch.r 649 kB/s | 16 kB 00:00 (63/81): perl-FindBin-1.54-514.el10.noarch.rpm 612 kB/s | 15 kB 00:00 (64/81): perl-Getopt-Std-1.14-514.el10.noarch.r 480 kB/s | 16 kB 00:00 (65/81): perl-IPC-Open3-1.22-514.el10.noarch.rp 937 kB/s | 23 kB 00:00 (66/81): perl-IO-1.55-514.el10.ppc64le.rpm 3.0 MB/s | 81 kB 00:00 (67/81): perl-Net-SSLeay-1.94-8.el10.ppc64le.rp 14 MB/s | 394 kB 00:00 (68/81): perl-SelectSaver-1.02-514.el10.noarch. 559 kB/s | 12 kB 00:00 (69/81): perl-POSIX-2.20-514.el10.ppc64le.rpm 3.5 MB/s | 99 kB 00:00 (70/81): perl-Symbol-1.09-514.el10.noarch.rpm 642 kB/s | 15 kB 00:00 (71/81): perl-base-2.27-514.el10.noarch.rpm 719 kB/s | 17 kB 00:00 (72/81): perl-if-0.61.000-514.el10.noarch.rpm 623 kB/s | 15 kB 00:00 (73/81): perl-interpreter-5.40.2-514.el10.ppc64 3.0 MB/s | 73 kB 00:00 (74/81): perl-lib-0.65-514.el10.ppc64le.rpm 682 kB/s | 16 kB 00:00 (75/81): perl-locale-1.12-514.el10.noarch.rpm 632 kB/s | 14 kB 00:00 (76/81): perl-libs-5.40.2-514.el10.ppc64le.rpm 44 MB/s | 2.5 MB 00:00 (77/81): perl-mro-1.29-514.el10.ppc64le.rpm 824 kB/s | 31 kB 00:00 (78/81): perl-overload-1.37-514.el10.noarch.rpm 1.8 MB/s | 46 kB 00:00 (79/81): perl-overloading-0.02-514.el10.noarch. 554 kB/s | 14 kB 00:00 (80/81): perl-vars-1.05-514.el10.noarch.rpm 554 kB/s | 14 kB 00:00 (81/81): zlib-ng-compat-devel-2.2.3-3.el10.ppc6 1.1 MB/s | 36 kB 00:00 -------------------------------------------------------------------------------- Total 14 MB/s | 61 MB 00:04 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.3.1-7.el10.ppc64le 1/81 Installing : htslib-1.23-1.el10.ppc64le 2/81 Installing : cpp-14.3.1-4.2.el10.ppc64le 3/81 Installing : ncurses-c++-libs-6.4-14.20240127.el10.ppc64le 4/81 Installing : libubsan-14.3.1-4.2.el10.ppc64le 5/81 Installing : libasan-14.3.1-4.2.el10.ppc64le 6/81 Installing : kernel-headers-6.12.0-191.el10.ppc64le 7/81 Installing : libxcrypt-devel-4.4.36-10.el10.ppc64le 8/81 Installing : glibc-devel-2.39-99.el10.ppc64le 9/81 Installing : cmake-filesystem-3.31.8-1.el10.ppc64le 10/81 Installing : annobin-docs-13.02-2.el10.noarch 11/81 Installing : ncurses-6.4-14.20240127.el10.ppc64le 12/81 Installing : make-1:4.4.1-9.el10.ppc64le 13/81 Installing : libatomic-14.3.1-4.2.el10.ppc64le 14/81 Installing : gcc-14.3.1-4.2.el10.ppc64le 15/81 Running scriptlet: gcc-14.3.1-4.2.el10.ppc64le 15/81 Running scriptlet: groff-base-1.23.0-10.el10.ppc64le 16/81 Installing : groff-base-1.23.0-10.el10.ppc64le 16/81 Running scriptlet: groff-base-1.23.0-10.el10.ppc64le 16/81 Installing : perl-Digest-1.20-511.el10.noarch 17/81 Installing : perl-Digest-MD5-2.59-6.el10.ppc64le 18/81 Installing : perl-B-1.89-514.el10.ppc64le 19/81 Installing : perl-FileHandle-2.05-514.el10.noarch 20/81 Installing : perl-Data-Dumper-2.189-512.el10.ppc64le 21/81 Installing : perl-libnet-3.15-512.el10.noarch 22/81 Installing : perl-AutoLoader-5.74-514.el10.noarch 23/81 Installing : perl-URI-5.27-3.el10.noarch 24/81 Installing : perl-Text-Tabs+Wrap-2024.001-511.el10.noarch 25/81 Installing : perl-Time-Local-2:1.350-511.el10.noarch 26/81 Installing : perl-Mozilla-CA-20231213-5.el10.noarch 27/81 Installing : perl-if-0.61.000-514.el10.noarch 28/81 Installing : perl-locale-1.12-514.el10.noarch 29/81 Installing : perl-IO-Socket-IP-0.42-512.el10.noarch 30/81 Installing : perl-Pod-Escapes-1:1.07-511.el10.noarch 31/81 Installing : perl-File-Path-2.18-512.el10.noarch 32/81 Installing : perl-IO-Socket-SSL-2.085-3.el10.noarch 33/81 Installing : perl-Net-SSLeay-1.94-8.el10.ppc64le 34/81 Installing : perl-Term-ANSIColor-5.01-512.el10.noarch 35/81 Installing : perl-Class-Struct-0.68-514.el10.noarch 36/81 Installing : perl-POSIX-2.20-514.el10.ppc64le 37/81 Installing : perl-IPC-Open3-1.22-514.el10.noarch 38/81 Installing : perl-Term-Cap-1.18-511.el10.noarch 39/81 Installing : perl-File-Temp-1:0.231.100-512.el10.noarch 40/81 Installing : perl-HTTP-Tiny-0.088-512.el10.noarch 41/81 Installing : perl-Pod-Simple-1:3.45-511.el10.noarch 42/81 Installing : perl-Socket-4:2.038-511.el10.ppc64le 43/81 Installing : perl-SelectSaver-1.02-514.el10.noarch 44/81 Installing : perl-Symbol-1.09-514.el10.noarch 45/81 Installing : perl-File-stat-1.14-514.el10.noarch 46/81 Installing : perl-podlators-1:5.01-511.el10.noarch 47/81 Installing : perl-Pod-Perldoc-3.28.01-512.el10.noarch 48/81 Installing : perl-Text-ParseWords-3.31-511.el10.noarch 49/81 Installing : perl-Fcntl-1.18-514.el10.ppc64le 50/81 Installing : perl-base-2.27-514.el10.noarch 51/81 Installing : perl-mro-1.29-514.el10.ppc64le 52/81 Installing : perl-IO-1.55-514.el10.ppc64le 53/81 Installing : perl-overloading-0.02-514.el10.noarch 54/81 Installing : perl-Pod-Usage-4:2.03-511.el10.noarch 55/81 Installing : perl-MIME-Base64-3.16-511.el10.ppc64le 56/81 Installing : perl-Scalar-List-Utils-5:1.63-511.el10.ppc64le 57/81 Installing : perl-constant-1.33-512.el10.noarch 58/81 Installing : perl-parent-1:0.241-512.el10.noarch 59/81 Installing : perl-Errno-1.38-514.el10.ppc64le 60/81 Installing : perl-File-Basename-2.86-514.el10.noarch 61/81 Installing : perl-Getopt-Std-1.14-514.el10.noarch 62/81 Installing : perl-Storable-1:3.32-511.el10.ppc64le 63/81 Installing : perl-overload-1.37-514.el10.noarch 64/81 Installing : perl-vars-1.05-514.el10.noarch 65/81 Installing : perl-Getopt-Long-1:2.58-3.el10.noarch 66/81 Installing : perl-Carp-1.54-511.el10.noarch 67/81 Installing : perl-Exporter-5.78-511.el10.noarch 68/81 Installing : perl-PathTools-3.91-512.el10.ppc64le 69/81 Installing : perl-DynaLoader-1.56-514.el10.ppc64le 70/81 Installing : perl-Encode-4:3.21-511.el10.ppc64le 71/81 Installing : perl-libs-4:5.40.2-514.el10.ppc64le 72/81 Installing : perl-interpreter-4:5.40.2-514.el10.ppc64le 73/81 Installing : perl-FindBin-1.54-514.el10.noarch 74/81 Installing : perl-lib-0.65-514.el10.ppc64le 75/81 Installing : annobin-plugin-gcc-13.02-2.el10.ppc64le 76/81 Running scriptlet: annobin-plugin-gcc-13.02-2.el10.ppc64le 76/81 Installing : gcc-plugin-annobin-14.3.1-4.2.el10.ppc64le 77/81 Running scriptlet: gcc-plugin-annobin-14.3.1-4.2.el10.ppc64le 77/81 Installing : zlib-ng-compat-devel-2.2.3-3.el10.ppc64le 78/81 Installing : ncurses-devel-6.4-14.20240127.el10.ppc64le 79/81 Installing : htslib-devel-1.23-1.el10.ppc64le 80/81 Installing : htslib-tools-1.23-1.el10.ppc64le 81/81 Running scriptlet: htslib-tools-1.23-1.el10.ppc64le 81/81 Installed: annobin-docs-13.02-2.el10.noarch annobin-plugin-gcc-13.02-2.el10.ppc64le cmake-filesystem-3.31.8-1.el10.ppc64le cpp-14.3.1-4.2.el10.ppc64le gcc-14.3.1-4.2.el10.ppc64le gcc-plugin-annobin-14.3.1-4.2.el10.ppc64le glibc-devel-2.39-99.el10.ppc64le groff-base-1.23.0-10.el10.ppc64le htslib-1.23-1.el10.ppc64le htslib-devel-1.23-1.el10.ppc64le htslib-tools-1.23-1.el10.ppc64le kernel-headers-6.12.0-191.el10.ppc64le libasan-14.3.1-4.2.el10.ppc64le libatomic-14.3.1-4.2.el10.ppc64le libmpc-1.3.1-7.el10.ppc64le libubsan-14.3.1-4.2.el10.ppc64le libxcrypt-devel-4.4.36-10.el10.ppc64le make-1:4.4.1-9.el10.ppc64le ncurses-6.4-14.20240127.el10.ppc64le ncurses-c++-libs-6.4-14.20240127.el10.ppc64le ncurses-devel-6.4-14.20240127.el10.ppc64le perl-AutoLoader-5.74-514.el10.noarch perl-B-1.89-514.el10.ppc64le perl-Carp-1.54-511.el10.noarch perl-Class-Struct-0.68-514.el10.noarch perl-Data-Dumper-2.189-512.el10.ppc64le perl-Digest-1.20-511.el10.noarch perl-Digest-MD5-2.59-6.el10.ppc64le perl-DynaLoader-1.56-514.el10.ppc64le perl-Encode-4:3.21-511.el10.ppc64le perl-Errno-1.38-514.el10.ppc64le perl-Exporter-5.78-511.el10.noarch perl-Fcntl-1.18-514.el10.ppc64le 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.ppc64le 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.ppc64le perl-Mozilla-CA-20231213-5.el10.noarch perl-Net-SSLeay-1.94-8.el10.ppc64le perl-POSIX-2.20-514.el10.ppc64le perl-PathTools-3.91-512.el10.ppc64le 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.ppc64le perl-SelectSaver-1.02-514.el10.noarch perl-Socket-4:2.038-511.el10.ppc64le perl-Storable-1:3.32-511.el10.ppc64le 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.ppc64le perl-lib-0.65-514.el10.ppc64le perl-libnet-3.15-512.el10.noarch perl-libs-4:5.40.2-514.el10.ppc64le perl-locale-1.12-514.el10.noarch perl-mro-1.29-514.el10.ppc64le 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.ppc64le Complete! Building target platforms: ppc64le Building for target ppc64le 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 5.8 kB/s | 1.5 kB 00:00 CentOS Stream 10 - BaseOS 319 kB/s | 22 kB 00:00 CentOS Stream 10 - AppStream 653 kB/s | 22 kB 00:00 CentOS Stream 10 - CRB 563 kB/s | 20 kB 00:00 CentOS Stream 10 - Extras packages 833 kB/s | 28 kB 00:00 Extra Packages for Enterprise Linux 10 - ppc64l 809 kB/s | 27 kB 00:00 Package gcc-14.3.1-4.2.el10.ppc64le is already installed. Package htslib-devel-1.23-1.el10.ppc64le is already installed. Package htslib-tools-1.23-1.el10.ppc64le is already installed. Package make-1:4.4.1-9.el10.ppc64le is already installed. Package ncurses-devel-6.4-14.20240127.el10.ppc64le 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.ppc64le is already installed. Package perl-interpreter-4:5.40.2-514.el10.ppc64le is already installed. Package zlib-ng-compat-devel-2.2.3-3.el10.ppc64le 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: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1769040000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.Vw6ezr + 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.ZGeJ1M + 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 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd samtools-1.23 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./htslib-1.23/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./htslib-1.23/config.guess ++ basename ./htslib-1.23/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./htslib-1.23/config.guess '/usr/lib/rpm/redhat/config.guess' -> './htslib-1.23/config.guess' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./htslib-1.23/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./htslib-1.23/config.sub ++ basename ./htslib-1.23/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./htslib-1.23/config.sub '/usr/lib/rpm/redhat/config.sub' -> './htslib-1.23/config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=ppc64le-redhat-linux --host=ppc64le-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 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --with-htslib=system checking for gawk... gawk checking for ppc64le-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 -j5 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 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_aux.o bam_aux.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_index.o bam_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_cat.o bam_cat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_plbuf.o bam_plbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_md.o bam_md.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_reheader.o bam_reheader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_fastq.o bam_fastq.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_plcmd.o bam_plcmd.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_view.o sam_view.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_rmdupse.o bam_rmdupse.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_stat.o bam_stat.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 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes "' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_rmdup.o bam_rmdup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_color.o bam_color.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 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam2bcf.o bam2bcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o cut_target.o cut_target.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sample.o sample.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_mate.o bam_mate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o coverage.o coverage.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o padding.o padding.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bedcov.o bedcov.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam2depth.o bam2depth.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o phase.o phase.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o dict.o dict.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_flags.o bam_flags.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o stats_isize.o stats_isize.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bamshuf.o bamshuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview_curses.o bam_tview_curses.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview.o bam_tview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_split.o bam_split.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview_html.o bam_tview_html.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_quickcheck.o bam_quickcheck.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_lpileup.o bam_lpileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_addrprg.o bam_addrprg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o tmp_file.o tmp_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_sort.o bam_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_import.o bam_import.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o stats.o stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_ampliconclip.o bam_ampliconclip.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_samples.o bam_samples.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o consensus_pileup.o consensus_pileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o reference.o reference.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o amplicon_stats.o amplicon_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o reset.o reset.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_markdup.o bam_markdup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o cram_size.o cram_size.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_opts.o sam_opts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_utils.o sam_utils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam.o bam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_consensus.o bam_consensus.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_checksum.o bam_checksum.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -DMAQ_LONGREADS -I. -I./lz4 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bedidx.o bedidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/md5fa.o misc/md5fa.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/test.o test/test.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/ace2sam.o misc/ace2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/wgsim.o misc/wgsim.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o lz4/lz4.o lz4/lz4.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bamtk.o bamtk.c ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_parse_args.o test/split/test_parse_args.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 -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 -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 -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o 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_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 -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 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.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 test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread 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 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o 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 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.G7B81G + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le '!=' / ']' + rm -rf /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le ++ dirname /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le + 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 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd samtools-1.23 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/share/man/man1 /usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/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.ppc64le/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.ppc64le/usr/bin /usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/share/man/man1 ++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/zoom2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/blast2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/bowtie2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/export2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/fasta-sanitize.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/interpolate_sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/novo2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/plot-ampliconstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/plot-bamstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/psl2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/sam2vcf.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/samtools.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/seq_cache_populate.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/soap2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/wgsim_eval.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/bin/zoom2sam.pl + /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 1.23-1.el10 --unique-debug-suffix -1.23-1.el10.ppc64le --unique-debug-src-base samtools-1.23-1.el10.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.23 find-debuginfo: starting Extracting debug info from 7 files DWARF-compressing 7 files sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/samtools-1.23-1.el10.ppc64le 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 -j5 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.x3JNQ4 + 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 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power10 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd samtools-1.23 + ldd samtools + grep -E -e '/lib(64)?/libhts\.so\.' -e '/lib64/lp64d/libhts\.so\.' libhts.so.3 => /lib64/libhts.so.3 (0x00007fff98b20000) + 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/R3fiKNVlQ9/bgzip.dat.gz .. ok bgzip -c -b 979200 -s 6 /tmp/R3fiKNVlQ9/bgzip.dat.gz .. ok bgzip -c -b 652804 -s 6 /tmp/R3fiKNVlQ9/bgzip.dat.gz .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/R3fiKNVlQ9/faidx.fa 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/R3fiKNVlQ9/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/R3fiKNVlQ9/faidx.fa 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/R3fiKNVlQ9/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/R3fiKNVlQ9/faidx.fa 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/R3fiKNVlQ9/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/R3fiKNVlQ9/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/R3fiKNVlQ9/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/R3fiKNVlQ9/fqidx.fq 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/R3fiKNVlQ9/fqidx.fq.gz 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/R3fiKNVlQ9/fqidx.fq 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/R3fiKNVlQ9/fqidx.fq.gz 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/R3fiKNVlQ9/fqidx.fq 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/R3fiKNVlQ9/fqidx.fq.gz 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/R3fiKNVlQ9/fqidx.fq 1:99998-100007 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/auto_indexed.csi && cat /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/auto_indexed.crai && cat /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/auto_indexed.csi && cat /tmp/R3fiKNVlQ9/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 /tmp/R3fiKNVlQ9/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/auto_indexed.csi && cat /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/auto_indexed.crai && cat /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/auto_indexed.csi && cat /tmp/R3fiKNVlQ9/auto_indexed.csi .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/R3fiKNVlQ9/mpileup.bam.list -f /tmp/R3fiKNVlQ9/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/R3fiKNVlQ9/mpileup.cram.list -f /tmp/R3fiKNVlQ9/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/R3fiKNVlQ9/mpileup.bam.urllist -f /tmp/R3fiKNVlQ9/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/R3fiKNVlQ9/mpileup.cram.urllist -f /tmp/R3fiKNVlQ9/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/R3fiKNVlQ9/mpileup.ref.fa.gz -r17:1050-1060 /tmp/R3fiKNVlQ9/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/R3fiKNVlQ9/mpileup.ref.fa.gz -r17:1050-1060 /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/R3fiKNVlQ9/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/R3fiKNVlQ9/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/R3fiKNVlQ9/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/R3fiKNVlQ9/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/R3fiKNVlQ9/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/R3fiKNVlQ9/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/R3fiKNVlQ9/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/R3fiKNVlQ9/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/R3fiKNVlQ9/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/R3fiKNVlQ9/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/R3fiKNVlQ9/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/R3fiKNVlQ9/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/R3fiKNVlQ9/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/R3fiKNVlQ9/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/R3fiKNVlQ9/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/R3fiKNVlQ9/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/R3fiKNVlQ9/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/R3fiKNVlQ9/view.001.forn (SAM input) .. ok 68: Count -N /tmp/R3fiKNVlQ9/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/R3fiKNVlQ9/view.001.forn (BAM input) .. ok 70: Count -N /tmp/R3fiKNVlQ9/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/R3fiKNVlQ9/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/R3fiKNVlQ9/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/R3fiKNVlQ9/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/R3fiKNVlQ9/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/R3fiKNVlQ9/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/R3fiKNVlQ9/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/R3fiKNVlQ9/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/R3fiKNVlQ9/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/R3fiKNVlQ9/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/R3fiKNVlQ9/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/R3fiKNVlQ9/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/R3fiKNVlQ9/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/R3fiKNVlQ9/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/R3fiKNVlQ9/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/R3fiKNVlQ9/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/R3fiKNVlQ9/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/R3fiKNVlQ9/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/R3fiKNVlQ9/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/R3fiKNVlQ9/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/R3fiKNVlQ9/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/R3fiKNVlQ9/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/R3fiKNVlQ9/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/R3fiKNVlQ9/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/view.test115.sam -h -d TGCA /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/R3fiKNVlQ9/view.test117.sam -h -d TGCA /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/R3fiKNVlQ9/view.test119.sam -h -d TGCA /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/R3fiKNVlQ9/view.001.fobc (SAM input) Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/R3fiKNVlQ9/view.test121.sam -h -D BClong:/tmp/R3fiKNVlQ9/view.001.fobc /tmp/R3fiKNVlQ9/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/R3fiKNVlQ9/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/R3fiKNVlQ9/view.001.fobc" samtools view: Invalid "tag:file" option: "BClong:/tmp/R3fiKNVlQ9/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/R3fiKNVlQ9/view.001.fobc /tmp/R3fiKNVlQ9/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/R3fiKNVlQ9/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/R3fiKNVlQ9/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/R3fiKNVlQ9/view.test123.sam -h -D BClong:/tmp/R3fiKNVlQ9/view.001.fobc /tmp/R3fiKNVlQ9/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/R3fiKNVlQ9/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/R3fiKNVlQ9/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/R3fiKNVlQ9/view.001.fobc /tmp/R3fiKNVlQ9/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/R3fiKNVlQ9/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/R3fiKNVlQ9/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/R3fiKNVlQ9/view.test125.sam -h -D BClong:/tmp/R3fiKNVlQ9/view.001.fobc /tmp/R3fiKNVlQ9/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/R3fiKNVlQ9/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/R3fiKNVlQ9/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/R3fiKNVlQ9/view.001.fobc /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/bam2fq.discard.s.fq -0 /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/bam2fq.discard.s.fq -0 /tmp/R3fiKNVlQ9/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/aJgr7d0cmQ - /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/R3fiKNVlQ9/merge.tag.1.bam /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/merge.tag.3.bam /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/merge.bed.1.bam /tmp/R3fiKNVlQ9/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/kGmuiDhXip - /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/R3fiKNVlQ9/merge.tag.1.bam /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/merge.tag.3.bam /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/merge.bed.1.bam /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /tmp/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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/R3fiKNVlQ9/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.ppc64le Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.w9qQ5l + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + DOCDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/share/doc/samtools + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/share/doc/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/AUTHORS /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/share/doc/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/ChangeLog.old /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/share/doc/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/NEWS.md /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/share/doc/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/examples /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/share/doc/samtools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.h0H8YZ + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/share/licenses/samtools + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/share/licenses/samtools + cp -pr /builddir/build/BUILD/samtools-1.23/LICENSE /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le/usr/share/licenses/samtools + RPM_EC=0 ++ jobs -p + exit 0 Provides: samtools = 1.23-1.el10 samtools(ppc-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_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.1)(64bit) libhts.so.3(HTSLIB_1.10)(64bit) libhts.so.3(HTSLIB_1.11)(64bit) libhts.so.3(HTSLIB_1.12)(64bit) libhts.so.3(HTSLIB_1.14)(64bit) libhts.so.3(HTSLIB_1.15)(64bit) libhts.so.3(HTSLIB_1.16)(64bit) libhts.so.3(HTSLIB_1.17)(64bit) libhts.so.3(HTSLIB_1.18)(64bit) libhts.so.3(HTSLIB_1.2.1)(64bit) libhts.so.3(HTSLIB_1.21)(64bit) libhts.so.3(HTSLIB_1.22)(64bit) libhts.so.3(HTSLIB_1.23)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) libhts.so.3(HTSLIB_1.9)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: samtools-debugsource-1.23-1.el10.ppc64le Provides: samtools-debugsource = 1.23-1.el10 samtools-debugsource(ppc-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.ppc64le Provides: debuginfo(build-id) = 17f2c2fd88d4adb65def57386694cfc72cd7bcb6 debuginfo(build-id) = 3d65dd90d3fd599f6a5ad370392b207de33107a3 debuginfo(build-id) = 91baac1c3f76570756963f5011508cc6c72904cd debuginfo(build-id) = a503f5f1dad9061118d9681826f2624d5ef568c7 debuginfo(build-id) = a8582f2bd034b794e1fca5a8556abcafd03aaff3 debuginfo(build-id) = bd16d54c80273273c99e11165f8f5e5fa829a2c3 debuginfo(build-id) = c696c6c9e25fae35426a30e3d39a25ae69e5565c samtools-debuginfo = 1.23-1.el10 samtools-debuginfo(ppc-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(ppc-64) = 1.23-1.el10 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le Wrote: /builddir/build/RPMS/samtools-1.23-1.el10.ppc64le.rpm Wrote: /builddir/build/RPMS/samtools-debugsource-1.23-1.el10.ppc64le.rpm Wrote: /builddir/build/RPMS/samtools-debuginfo-1.23-1.el10.ppc64le.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.NIC0WM + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.23-1.el10.ppc64le + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.AT1afD + 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-ppc64le-1769509936.247694/root/var/log/dnf.rpm.log /var/lib/mock/centos-stream+epel-10-ppc64le-1769509936.247694/root/var/log/dnf.librepo.log /var/lib/mock/centos-stream+epel-10-ppc64le-1769509936.247694/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 54 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": "src" }, { "name": "samtools-debuginfo", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "ppc64le" }, { "name": "samtools", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "ppc64le" }, { "name": "samtools-debugsource", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "ppc64le" } ] } RPMResults finished