Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c1ce' (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/7524287-epel-9-x86_64 --chroot epel-9-x86_64 Version: 0.73 PID: 7040 Logging PID: 7041 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'bootstrap': 'off', 'build_id': 7524287, 'buildroot_pkgs': [], 'chroot': 'epel-9-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '41ea07c25de28e8ce206f694a72102f43a04ecb0', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/yamaura/genomics/samtools', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'samtools', 'package_version': '1.20-1', 'project_dirname': 'genomics', 'project_name': 'genomics', 'project_owner': 'yamaura', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/yamaura/genomics/epel-9-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'yamaura/genomics--yamaura', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'submitter': 'yamaura', 'tags': [], 'task_id': '7524287-epel-9-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/yamaura/genomics/samtools /var/lib/copr-rpmbuild/workspace/workdir-5rh5i_yn/samtools --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/yamaura/genomics/samtools', '/var/lib/copr-rpmbuild/workspace/workdir-5rh5i_yn/samtools', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-5rh5i_yn/samtools'... Running: git checkout 41ea07c25de28e8ce206f694a72102f43a04ecb0 -- cmd: ['git', 'checkout', '41ea07c25de28e8ce206f694a72102f43a04ecb0', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-5rh5i_yn/samtools rc: 0 stdout: stderr: Note: switching to '41ea07c25de28e8ce206f694a72102f43a04ecb0'. 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 41ea07c automatic import of samtools Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-5rh5i_yn/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-1.20.tar.bz2 INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o samtools-1.20.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/yamaura/genomics/samtools/samtools-1.20.tar.bz2/md5/e33f429b57324a55e5cbe0ef9f3a094e/samtools-1.20.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 8964k 100 8964k 0 0 56.0M 0 --:--:-- --:--:-- --:--:-- 56.4M INFO: Reading stdout from command: md5sum samtools-1.20.tar.bz2 /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-5rh5i_yn/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-5rh5i_yn/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1717413963.379560 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.6 starting (python version = 3.12.1, NVR = mock-5.6-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-5rh5i_yn/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-5rh5i_yn/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1717413963.379560 -r /var/lib/copr-rpmbuild/results/configs/child.cfg 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-5rh5i_yn/samtools/samtools.spec) Config(rhel+epel-9-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.6 INFO: Mock Version: 5.6 Start: chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-x86_64-1717413963.379560/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 dnf detected and used (fallback) INFO: Buildroot is handled by package management from host and used with --installroot: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.19.2-1.fc39.noarch python3-dnf-plugins-core-4.6.0-1.fc39.noarch yum-4.19.2-1.fc39.noarch dnf5-5.1.17-1.fc39.x86_64 dnf5-plugins-5.1.17-1.fc39.x86_64 Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 102 kB/s | 17 kB 00:00 Red Hat Enterprise Linux - BaseOS 20 MB/s | 22 MB 00:01 Red Hat Enterprise Linux - AppStream 24 kB/s | 35 MB 25:18 Red Hat Enterprise Linux - CodeReady Linux Buil 12 MB/s | 7.8 MB 00:00 Extra Packages for Enterprise Linux 9 - x86_64 19 MB/s | 21 MB 00:01 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: bash x86_64 5.1.8-9.el9 baseos 1.7 M bzip2 x86_64 1.0.8-8.el9 baseos 60 k coreutils x86_64 8.32-35.el9 baseos 1.2 M cpio x86_64 2.13-16.el9 baseos 279 k diffutils x86_64 3.7-12.el9 baseos 402 k epel-rpm-macros noarch 9-14.el9 epel 15 k findutils x86_64 1:4.8.0-6.el9 baseos 550 k gawk x86_64 5.1.0-6.el9 baseos 1.0 M glibc-minimal-langpack x86_64 2.34-100.el9_4.2 baseos 28 k grep x86_64 3.6-5.el9 baseos 273 k gzip x86_64 1.12-1.el9 baseos 167 k info x86_64 6.7-15.el9 baseos 228 k patch x86_64 2.7.6-16.el9 appstream 130 k redhat-release x86_64 9.4-0.4.el9 baseos 46 k redhat-rpm-config noarch 207-1.el9 appstream 76 k rpm-build x86_64 4.16.1.3-29.el9 appstream 72 k sed x86_64 4.8-9.el9 baseos 309 k tar x86_64 2:1.34-6.el9_1 baseos 889 k unzip x86_64 6.0-56.el9 baseos 186 k util-linux x86_64 2.37.4-18.el9 baseos 2.3 M which x86_64 2.21-29.el9 baseos 45 k xz x86_64 5.2.5-8.el9_0 baseos 230 k Installing dependencies: alternatives x86_64 1.24-1.el9 baseos 42 k ansible-srpm-macros noarch 1-12.el9 epel 21 k audit-libs x86_64 3.1.2-2.el9 baseos 121 k basesystem noarch 11-13.el9 baseos 8.0 k binutils x86_64 2.35.2-43.el9 baseos 4.6 M binutils-gold x86_64 2.35.2-43.el9 baseos 736 k bzip2-libs x86_64 1.0.8-8.el9 baseos 42 k ca-certificates noarch 2023.2.60_v7.0.306-90.1.el9_2 baseos 846 k coreutils-common x86_64 8.32-35.el9 baseos 2.0 M cracklib x86_64 2.9.6-27.el9 baseos 99 k cracklib-dicts x86_64 2.9.6-27.el9 baseos 3.6 M crypto-policies noarch 20240202-1.git283706d.el9 baseos 88 k curl x86_64 7.76.1-29.el9_4 baseos 298 k cyrus-sasl-lib x86_64 2.1.27-21.el9 baseos 774 k debugedit x86_64 5.0-5.el9 appstream 81 k dwz x86_64 0.14-3.el9 appstream 130 k ed x86_64 1.14.2-12.el9 baseos 78 k efi-srpm-macros noarch 6-2.el9_0 appstream 24 k elfutils x86_64 0.190-2.el9 baseos 559 k elfutils-debuginfod-client x86_64 0.190-2.el9 baseos 39 k elfutils-default-yama-scope noarch 0.190-2.el9 baseos 12 k elfutils-libelf x86_64 0.190-2.el9 baseos 196 k elfutils-libs x86_64 0.190-2.el9 baseos 258 k file x86_64 5.39-16.el9 baseos 52 k file-libs x86_64 5.39-16.el9 baseos 593 k filesystem x86_64 3.16-2.el9 baseos 4.7 M fonts-srpm-macros noarch 1:2.0.5-7.el9.1 appstream 29 k forge-srpm-macros noarch 0.3.1-1.el9 epel 19 k fpc-srpm-macros noarch 1.3-7.el9 epel 7.5 k gdb-minimal x86_64 10.2-13.el9 appstream 3.5 M gdbm-libs x86_64 1:1.19-4.el9 baseos 56 k ghc-srpm-macros noarch 1.5.0-6.el9 appstream 9.0 k glibc x86_64 2.34-100.el9_4.2 baseos 2.0 M glibc-common x86_64 2.34-100.el9_4.2 baseos 313 k glibc-gconv-extra x86_64 2.34-100.el9_4.2 baseos 1.7 M gmp x86_64 1:6.2.0-13.el9 baseos 319 k go-srpm-macros noarch 3.2.0-3.el9 appstream 28 k go-srpm-macros-epel noarch 3.3.0.5-1.el9 epel 27 k groff-base x86_64 1.22.4-10.el9 baseos 1.1 M kernel-srpm-macros noarch 1.0-13.el9 appstream 17 k keyutils-libs x86_64 1.6.3-1.el9 baseos 34 k krb5-libs x86_64 1.21.1-1.el9 baseos 770 k libacl x86_64 2.3.1-4.el9 baseos 24 k libarchive x86_64 3.5.3-4.el9 baseos 392 k libattr x86_64 2.5.1-3.el9 baseos 20 k libblkid x86_64 2.37.4-18.el9 baseos 110 k libbrotli x86_64 1.0.9-6.el9 baseos 317 k libcap x86_64 2.48-9.el9_2 baseos 74 k libcap-ng x86_64 0.8.2-7.el9 baseos 36 k libcom_err x86_64 1.46.5-5.el9 baseos 28 k libcurl x86_64 7.76.1-29.el9_4 baseos 286 k libdb x86_64 5.3.28-53.el9 baseos 740 k libeconf x86_64 0.4.1-3.el9_2 baseos 30 k libevent x86_64 2.1.12-6.el9 baseos 268 k libfdisk x86_64 2.37.4-18.el9 baseos 157 k libffi x86_64 3.4.2-8.el9 baseos 40 k libgcc x86_64 11.4.1-3.el9 baseos 95 k libgcrypt x86_64 1.10.0-10.el9_2 baseos 508 k libgomp x86_64 11.4.1-3.el9 baseos 270 k libgpg-error x86_64 1.42-5.el9 baseos 220 k libidn2 x86_64 2.3.0-7.el9 baseos 105 k libmount x86_64 2.37.4-18.el9 baseos 138 k libnghttp2 x86_64 1.43.0-5.el9_4.3 baseos 75 k libpkgconf x86_64 1.7.3-10.el9 baseos 37 k libpsl x86_64 0.21.1-5.el9 baseos 66 k libpwquality x86_64 1.4.4-8.el9 baseos 123 k libselinux x86_64 3.6-1.el9 baseos 88 k libsemanage x86_64 3.6-1.el9 baseos 121 k libsepol x86_64 3.6-1.el9 baseos 331 k libsigsegv x86_64 2.13-4.el9 baseos 30 k libsmartcols x86_64 2.37.4-18.el9 baseos 66 k libssh x86_64 0.10.4-13.el9 baseos 220 k libssh-config noarch 0.10.4-13.el9 baseos 11 k libstdc++ x86_64 11.4.1-3.el9 baseos 747 k libtasn1 x86_64 4.16.0-8.el9_1 baseos 77 k libunistring x86_64 0.9.10-15.el9 baseos 499 k libutempter x86_64 1.2.1-6.el9 baseos 30 k libuuid x86_64 2.37.4-18.el9 baseos 30 k libverto x86_64 0.3.2-3.el9 baseos 24 k libxcrypt x86_64 4.4.18-3.el9 baseos 120 k libxml2 x86_64 2.9.13-6.el9_4 baseos 752 k libzstd x86_64 1.5.1-2.el9 baseos 332 k lua-libs x86_64 5.4.4-4.el9 baseos 132 k lua-srpm-macros noarch 1-6.el9 appstream 10 k lz4-libs x86_64 1.9.3-5.el9 baseos 69 k mpfr x86_64 4.1.0-7.el9 baseos 329 k ncurses x86_64 6.2-10.20210508.el9 baseos 410 k ncurses-base noarch 6.2-10.20210508.el9 baseos 99 k ncurses-libs x86_64 6.2-10.20210508.el9 baseos 332 k ocaml-srpm-macros noarch 6-6.el9 appstream 9.1 k openblas-srpm-macros noarch 2-11.el9 appstream 8.6 k openldap x86_64 2.6.6-3.el9 baseos 286 k openssl x86_64 1:3.0.7-27.el9 baseos 1.2 M openssl-fips-provider x86_64 3.0.7-2.el9 baseos 576 k openssl-libs x86_64 1:3.0.7-27.el9 baseos 1.9 M p11-kit x86_64 0.25.3-2.el9 baseos 537 k p11-kit-trust x86_64 0.25.3-2.el9 baseos 145 k pam x86_64 1.5.1-19.el9 baseos 631 k pcre x86_64 8.44-3.el9.3 baseos 202 k pcre2 x86_64 10.40-5.el9 baseos 236 k pcre2-syntax noarch 10.40-5.el9 baseos 145 k perl-AutoLoader noarch 5.74-481.el9 appstream 21 k perl-B x86_64 1.80-481.el9 appstream 184 k perl-Carp noarch 1.50-460.el9 appstream 31 k perl-Class-Struct noarch 0.66-481.el9 appstream 22 k perl-Data-Dumper x86_64 2.174-462.el9 appstream 59 k perl-Digest noarch 1.19-4.el9 appstream 29 k perl-Digest-MD5 x86_64 2.58-4.el9 appstream 39 k perl-Encode x86_64 4:3.08-462.el9 appstream 1.7 M perl-Errno x86_64 1.30-481.el9 appstream 15 k perl-Exporter noarch 5.74-461.el9 appstream 34 k perl-Fcntl x86_64 1.13-481.el9 appstream 22 k perl-File-Basename noarch 2.85-481.el9 appstream 17 k perl-File-Path noarch 2.18-4.el9 appstream 38 k perl-File-Temp noarch 1:0.231.100-4.el9 appstream 63 k perl-File-stat noarch 1.09-481.el9 appstream 17 k perl-FileHandle noarch 2.03-481.el9 appstream 16 k perl-Getopt-Long noarch 1:2.52-4.el9 appstream 64 k perl-Getopt-Std noarch 1.12-481.el9 appstream 16 k perl-HTTP-Tiny noarch 0.076-462.el9 appstream 57 k perl-IO x86_64 1.43-481.el9 appstream 92 k perl-IO-Socket-IP noarch 0.41-5.el9 appstream 45 k perl-IO-Socket-SSL noarch 2.073-1.el9 appstream 223 k perl-IPC-Open3 noarch 1.21-481.el9 appstream 24 k perl-MIME-Base64 x86_64 3.16-4.el9 appstream 34 k perl-Mozilla-CA noarch 20200520-6.el9 appstream 14 k perl-Net-SSLeay x86_64 1.92-2.el9 appstream 392 k perl-POSIX x86_64 1.94-481.el9 appstream 98 k perl-PathTools x86_64 3.78-461.el9 appstream 92 k perl-Pod-Escapes noarch 1:1.07-460.el9 appstream 22 k perl-Pod-Perldoc noarch 3.28.01-461.el9 appstream 92 k perl-Pod-Simple noarch 1:3.42-4.el9 appstream 229 k perl-Pod-Usage noarch 4:2.01-4.el9 appstream 43 k perl-Scalar-List-Utils x86_64 4:1.56-461.el9 appstream 77 k perl-SelectSaver noarch 1.02-481.el9 appstream 12 k perl-Socket x86_64 4:2.031-4.el9 appstream 58 k perl-Storable x86_64 1:3.21-460.el9 appstream 98 k perl-Symbol noarch 1.08-481.el9 appstream 14 k perl-Term-ANSIColor noarch 5.01-461.el9 appstream 51 k perl-Term-Cap noarch 1.17-460.el9 appstream 24 k perl-Text-ParseWords noarch 3.30-460.el9 appstream 18 k perl-Text-Tabs+Wrap noarch 2013.0523-460.el9 appstream 25 k perl-Time-Local noarch 2:1.300-7.el9 appstream 37 k perl-URI noarch 5.09-3.el9 appstream 125 k perl-base noarch 2.27-481.el9 appstream 16 k perl-constant noarch 1.33-461.el9 appstream 25 k perl-if noarch 0.60.800-481.el9 appstream 14 k perl-interpreter x86_64 4:5.32.1-481.el9 appstream 73 k perl-libnet noarch 3.13-4.el9 appstream 134 k perl-libs x86_64 4:5.32.1-481.el9 appstream 2.2 M perl-mro x86_64 1.23-481.el9 appstream 29 k perl-overload noarch 1.31-481.el9 appstream 46 k perl-overloading noarch 0.02-481.el9 appstream 13 k perl-parent noarch 1:0.238-460.el9 appstream 16 k perl-podlators noarch 1:4.14-460.el9 appstream 118 k perl-srpm-macros noarch 1-41.el9 appstream 9.4 k perl-subs noarch 1.03-481.el9 appstream 12 k perl-vars noarch 1.05-481.el9 appstream 13 k pkgconf x86_64 1.7.3-10.el9 baseos 45 k pkgconf-m4 noarch 1.7.3-10.el9 baseos 16 k pkgconf-pkg-config x86_64 1.7.3-10.el9 baseos 12 k popt x86_64 1.18-8.el9 baseos 69 k publicsuffix-list-dafsa noarch 20210518-3.el9 baseos 59 k pyproject-srpm-macros noarch 1.12.0-1.el9 appstream 14 k python-srpm-macros noarch 3.9-53.el9 appstream 19 k qt5-srpm-macros noarch 5.15.9-1.el9 appstream 9.1 k qt6-srpm-macros noarch 6.6.2-1.el9 epel 8.7 k readline x86_64 8.1-4.el9 baseos 215 k rpm x86_64 4.16.1.3-29.el9 baseos 541 k rpm-build-libs x86_64 4.16.1.3-29.el9 baseos 90 k rpm-libs x86_64 4.16.1.3-29.el9 baseos 310 k rpmautospec-rpm-macros noarch 0.6.3-1.el9 epel 9.9 k rust-srpm-macros noarch 17-4.el9 appstream 11 k rust-srpm-macros-epel noarch 26.3-1.el9 epel 10 k setup noarch 2.13.7-10.el9 baseos 150 k shadow-utils x86_64 2:4.9-8.el9 baseos 1.2 M sqlite-libs x86_64 3.34.1-7.el9_3 baseos 622 k systemd-libs x86_64 252-32.el9_4 baseos 679 k tzdata noarch 2024a-1.el9 baseos 842 k util-linux-core x86_64 2.37.4-18.el9 baseos 469 k xz-libs x86_64 5.2.5-8.el9_0 baseos 94 k zip x86_64 3.0-35.el9 baseos 270 k zlib x86_64 1.2.11-40.el9 baseos 93 k zstd x86_64 1.5.1-2.el9 baseos 552 k Transaction Summary ================================================================================ Install 206 Packages Total download size: 68 M Installed size: 215 M Downloading Packages: (1/206): basesystem-11-13.el9.noarch.rpm 48 kB/s | 8.0 kB 00:00 (2/206): bzip2-libs-1.0.8-8.el9.x86_64.rpm 247 kB/s | 42 kB 00:00 (3/206): bzip2-1.0.8-8.el9.x86_64.rpm 251 kB/s | 60 kB 00:00 (4/206): cpio-2.13-16.el9.x86_64.rpm 1.7 MB/s | 279 kB 00:00 (5/206): cracklib-2.9.6-27.el9.x86_64.rpm 575 kB/s | 99 kB 00:00 (6/206): ed-1.14.2-12.el9.x86_64.rpm 717 kB/s | 78 kB 00:00 (7/206): grep-3.6-5.el9.x86_64.rpm 2.5 MB/s | 273 kB 00:00 (8/206): groff-base-1.22.4-10.el9.x86_64.rpm 6.1 MB/s | 1.1 MB 00:00 (9/206): info-6.7-15.el9.x86_64.rpm 2.0 MB/s | 228 kB 00:00 (10/206): filesystem-3.16-2.el9.x86_64.rpm 14 MB/s | 4.7 MB 00:00 (11/206): libbrotli-1.0.9-6.el9.x86_64.rpm 2.7 MB/s | 317 kB 00:00 (12/206): libcap-ng-0.8.2-7.el9.x86_64.rpm 466 kB/s | 36 kB 00:00 (13/206): libdb-5.3.28-53.el9.x86_64.rpm 7.5 MB/s | 740 kB 00:00 (14/206): libevent-2.1.12-6.el9.x86_64.rpm 2.2 MB/s | 268 kB 00:00 (15/206): libgpg-error-1.42-5.el9.x86_64.rpm 2.3 MB/s | 220 kB 00:00 (16/206): libpsl-0.21.1-5.el9.x86_64.rpm 730 kB/s | 66 kB 00:00 (17/206): libidn2-2.3.0-7.el9.x86_64.rpm 1.0 MB/s | 105 kB 00:00 (18/206): libpwquality-1.4.4-8.el9.x86_64.rpm 1.6 MB/s | 123 kB 00:00 (19/206): libattr-2.5.1-3.el9.x86_64.rpm 40 kB/s | 20 kB 00:00 (20/206): libsigsegv-2.13-4.el9.x86_64.rpm 266 kB/s | 30 kB 00:00 (21/206): libutempter-1.2.1-6.el9.x86_64.rpm 416 kB/s | 30 kB 00:00 (22/206): libverto-0.3.2-3.el9.x86_64.rpm 250 kB/s | 24 kB 00:00 (23/206): libunistring-0.9.10-15.el9.x86_64.rpm 3.3 MB/s | 499 kB 00:00 (24/206): libxcrypt-4.4.18-3.el9.x86_64.rpm 1.6 MB/s | 120 kB 00:00 (25/206): libzstd-1.5.1-2.el9.x86_64.rpm 4.1 MB/s | 332 kB 00:00 (26/206): mpfr-4.1.0-7.el9.x86_64.rpm 2.8 MB/s | 329 kB 00:00 (27/206): lz4-libs-1.9.3-5.el9.x86_64.rpm 376 kB/s | 69 kB 00:00 (28/206): pcre-8.44-3.el9.3.x86_64.rpm 1.5 MB/s | 202 kB 00:00 (29/206): popt-1.18-8.el9.x86_64.rpm 761 kB/s | 69 kB 00:00 (30/206): publicsuffix-list-dafsa-20210518-3.el 640 kB/s | 59 kB 00:00 (31/206): unzip-6.0-56.el9.x86_64.rpm 2.3 MB/s | 186 kB 00:00 (32/206): sed-4.8-9.el9.x86_64.rpm 1.6 MB/s | 309 kB 00:00 (33/206): readline-8.1-4.el9.x86_64.rpm 1.0 MB/s | 215 kB 00:00 (34/206): diffutils-3.7-12.el9.x86_64.rpm 3.8 MB/s | 402 kB 00:00 (35/206): cracklib-dicts-2.9.6-27.el9.x86_64.rp 13 MB/s | 3.6 MB 00:00 (36/206): gawk-5.1.0-6.el9.x86_64.rpm 4.0 MB/s | 1.0 MB 00:00 (37/206): xz-5.2.5-8.el9_0.x86_64.rpm 1.7 MB/s | 230 kB 00:00 (38/206): xz-libs-5.2.5-8.el9_0.x86_64.rpm 750 kB/s | 94 kB 00:00 (39/206): gdbm-libs-1.19-4.el9.x86_64.rpm 193 kB/s | 56 kB 00:00 (40/206): gzip-1.12-1.el9.x86_64.rpm 1.1 MB/s | 167 kB 00:00 (41/206): zstd-1.5.1-2.el9.x86_64.rpm 2.9 MB/s | 552 kB 00:00 (42/206): cyrus-sasl-lib-2.1.27-21.el9.x86_64.r 4.2 MB/s | 774 kB 00:00 (43/206): libtasn1-4.16.0-8.el9_1.x86_64.rpm 1.1 MB/s | 77 kB 00:00 (44/206): tar-1.34-6.el9_1.x86_64.rpm 11 MB/s | 889 kB 00:00 (45/206): ca-certificates-2023.2.60_v7.0.306-90 8.6 MB/s | 846 kB 00:00 (46/206): keyutils-libs-1.6.3-1.el9.x86_64.rpm 508 kB/s | 34 kB 00:00 (47/206): libarchive-3.5.3-4.el9.x86_64.rpm 4.6 MB/s | 392 kB 00:00 (48/206): libcap-2.48-9.el9_2.x86_64.rpm 1.1 MB/s | 74 kB 00:00 (49/206): libeconf-0.4.1-3.el9_2.x86_64.rpm 439 kB/s | 30 kB 00:00 (50/206): libpkgconf-1.7.3-10.el9.x86_64.rpm 480 kB/s | 37 kB 00:00 (51/206): pkgconf-1.7.3-10.el9.x86_64.rpm 671 kB/s | 45 kB 00:00 (52/206): libgcrypt-1.10.0-10.el9_2.x86_64.rpm 4.2 MB/s | 508 kB 00:00 (53/206): pkgconf-m4-1.7.3-10.el9.noarch.rpm 167 kB/s | 16 kB 00:00 (54/206): pkgconf-pkg-config-1.7.3-10.el9.x86_6 119 kB/s | 12 kB 00:00 (55/206): alternatives-1.24-1.el9.x86_64.rpm 579 kB/s | 42 kB 00:00 (56/206): zip-3.0-35.el9.x86_64.rpm 2.0 MB/s | 270 kB 00:00 (57/206): findutils-4.8.0-6.el9.x86_64.rpm 6.0 MB/s | 550 kB 00:00 (58/206): gmp-6.2.0-13.el9.x86_64.rpm 4.5 MB/s | 319 kB 00:00 (59/206): libffi-3.4.2-8.el9.x86_64.rpm 490 kB/s | 40 kB 00:00 (60/206): krb5-libs-1.21.1-1.el9.x86_64.rpm 4.9 MB/s | 770 kB 00:00 (61/206): lua-libs-5.4.4-4.el9.x86_64.rpm 1.5 MB/s | 132 kB 00:00 (62/206): ncurses-6.2-10.20210508.el9.x86_64.rp 4.9 MB/s | 410 kB 00:00 (63/206): ncurses-base-6.2-10.20210508.el9.noar 1.4 MB/s | 99 kB 00:00 (64/206): shadow-utils-4.9-8.el9.x86_64.rpm 11 MB/s | 1.2 MB 00:00 (65/206): ncurses-libs-6.2-10.20210508.el9.x86_ 2.1 MB/s | 332 kB 00:00 (66/206): which-2.21-29.el9.x86_64.rpm 417 kB/s | 45 kB 00:00 (67/206): zlib-1.2.11-40.el9.x86_64.rpm 1.4 MB/s | 93 kB 00:00 (68/206): audit-libs-3.1.2-2.el9.x86_64.rpm 1.2 MB/s | 121 kB 00:00 (69/206): bash-5.1.8-9.el9.x86_64.rpm 18 MB/s | 1.7 MB 00:00 (70/206): binutils-2.35.2-43.el9.x86_64.rpm 32 MB/s | 4.6 MB 00:00 (71/206): binutils-gold-2.35.2-43.el9.x86_64.rp 5.1 MB/s | 736 kB 00:00 (72/206): curl-7.76.1-29.el9_4.x86_64.rpm 4.3 MB/s | 298 kB 00:00 (73/206): coreutils-8.32-35.el9.x86_64.rpm 6.1 MB/s | 1.2 MB 00:00 (74/206): coreutils-common-8.32-35.el9.x86_64.r 16 MB/s | 2.0 MB 00:00 (75/206): elfutils-0.190-2.el9.x86_64.rpm 5.7 MB/s | 559 kB 00:00 (76/206): elfutils-default-yama-scope-0.190-2.e 127 kB/s | 12 kB 00:00 (77/206): file-5.39-16.el9.x86_64.rpm 680 kB/s | 52 kB 00:00 (78/206): file-libs-5.39-16.el9.x86_64.rpm 7.3 MB/s | 593 kB 00:00 (79/206): elfutils-libs-0.190-2.el9.x86_64.rpm 1.4 MB/s | 258 kB 00:00 (80/206): libacl-2.3.1-4.el9.x86_64.rpm 357 kB/s | 24 kB 00:00 (81/206): libfdisk-2.37.4-18.el9.x86_64.rpm 2.3 MB/s | 157 kB 00:00 (82/206): libgcc-11.4.1-3.el9.x86_64.rpm 1.3 MB/s | 95 kB 00:00 (83/206): libgomp-11.4.1-3.el9.x86_64.rpm 3.9 MB/s | 270 kB 00:00 (84/206): libmount-2.37.4-18.el9.x86_64.rpm 1.9 MB/s | 138 kB 00:00 (85/206): libblkid-2.37.4-18.el9.x86_64.rpm 506 kB/s | 110 kB 00:00 (86/206): libselinux-3.6-1.el9.x86_64.rpm 1.3 MB/s | 88 kB 00:00 (87/206): libsemanage-3.6-1.el9.x86_64.rpm 1.8 MB/s | 121 kB 00:00 (88/206): libsmartcols-2.37.4-18.el9.x86_64.rpm 970 kB/s | 66 kB 00:00 (89/206): libstdc++-11.4.1-3.el9.x86_64.rpm 9.2 MB/s | 747 kB 00:00 (90/206): libuuid-2.37.4-18.el9.x86_64.rpm 467 kB/s | 30 kB 00:00 (91/206): libsepol-3.6-1.el9.x86_64.rpm 1.8 MB/s | 331 kB 00:00 (92/206): openldap-2.6.6-3.el9.x86_64.rpm 4.1 MB/s | 286 kB 00:00 (93/206): openssl-3.0.7-27.el9.x86_64.rpm 11 MB/s | 1.2 MB 00:00 (94/206): openssl-fips-provider-3.0.7-2.el9.x86 7.5 MB/s | 576 kB 00:00 (95/206): openssl-libs-3.0.7-27.el9.x86_64.rpm 15 MB/s | 1.9 MB 00:00 (96/206): p11-kit-trust-0.25.3-2.el9.x86_64.rpm 1.7 MB/s | 145 kB 00:00 (97/206): p11-kit-0.25.3-2.el9.x86_64.rpm 4.6 MB/s | 537 kB 00:00 (98/206): pam-1.5.1-19.el9.x86_64.rpm 8.7 MB/s | 631 kB 00:00 (99/206): pcre2-10.40-5.el9.x86_64.rpm 2.5 MB/s | 236 kB 00:00 (100/206): rpm-4.16.1.3-29.el9.x86_64.rpm 7.0 MB/s | 541 kB 00:00 (101/206): rpm-build-libs-4.16.1.3-29.el9.x86_6 1.0 MB/s | 90 kB 00:00 (102/206): setup-2.13.7-10.el9.noarch.rpm 2.1 MB/s | 150 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(117/206): redhat-release-9.4-0.4.el9.x86_64.rp 450 kB/s | 46 kB 00:00 (118/206): glibc-common-2.34-100.el9_4.2.x86_64 3.2 MB/s | 313 kB 00:00 (119/206): glibc-2.34-100.el9_4.2.x86_64.rpm 8.7 MB/s | 2.0 MB 00:00 (120/206): libxml2-2.9.13-6.el9_4.x86_64.rpm 2.6 MB/s | 752 kB 00:00 (121/206): glibc-gconv-extra-2.34-100.el9_4.2.x 10 MB/s | 1.7 MB 00:00 (122/206): libnghttp2-1.43.0-5.el9_4.3.x86_64.r 903 kB/s | 75 kB 00:00 (123/206): glibc-minimal-langpack-2.34-100.el9_ 249 kB/s | 28 kB 00:00 (124/206): ghc-srpm-macros-1.5.0-6.el9.noarch.r 117 kB/s | 9.0 kB 00:00 (125/206): lua-srpm-macros-1-6.el9.noarch.rpm 152 kB/s | 10 kB 00:00 (126/206): perl-Digest-MD5-2.58-4.el9.x86_64.rp 565 kB/s | 39 kB 00:00 (127/206): perl-Encode-3.08-462.el9.x86_64.rpm 17 MB/s | 1.7 MB 00:00 (128/206): perl-IO-Socket-SSL-2.073-1.el9.noarc 3.1 MB/s | 223 kB 00:00 (129/206): perl-Data-Dumper-2.174-462.el9.x86_6 290 kB/s | 59 kB 00:00 (130/206): perl-Term-Cap-1.17-460.el9.noarch.rp 334 kB/s | 24 kB 00:00 (131/206): perl-Pod-Simple-3.42-4.el9.noarch.rp 2.8 MB/s | 229 kB 00:00 (132/206): perl-Mozilla-CA-20200520-6.el9.noarc 97 kB/s | 14 kB 00:00 (133/206): rust-srpm-macros-17-4.el9.noarch.rpm 167 kB/s | 11 kB 00:00 (134/206): perl-Time-Local-1.300-7.el9.noarch.r 365 kB/s | 37 kB 00:00 (135/206): perl-Pod-Escapes-1.07-460.el9.noarch 287 kB/s | 22 kB 00:00 (136/206): perl-Storable-3.21-460.el9.x86_64.rp 1.5 MB/s | 98 kB 00:00 (137/206): perl-podlators-4.14-460.el9.noarch.r 1.8 MB/s | 118 kB 00:00 (138/206): dwz-0.14-3.el9.x86_64.rpm 1.8 MB/s | 130 kB 00:00 (139/206): perl-Exporter-5.74-461.el9.noarch.rp 518 kB/s | 34 kB 00:00 (140/206): perl-Getopt-Long-2.52-4.el9.noarch.r 955 kB/s | 64 kB 00:00 (141/206): perl-MIME-Base64-3.16-4.el9.x86_64.r 338 kB/s | 34 kB 00:00 (142/206): perl-File-Temp-0.231.100-4.el9.noarc 429 kB/s | 63 kB 00:00 (143/206): perl-Text-Tabs+Wrap-2013.0523-460.el 368 kB/s | 25 kB 00:00 (144/206): perl-parent-0.238-460.el9.noarch.rpm 242 kB/s | 16 kB 00:00 (145/206): efi-srpm-macros-6-2.el9_0.noarch.rpm 349 kB/s | 24 kB 00:00 (146/206): perl-srpm-macros-1-41.el9.noarch.rpm 97 kB/s | 9.4 kB 00:00 (147/206): openblas-srpm-macros-2-11.el9.noarch 131 kB/s | 8.6 kB 00:00 (148/206): perl-File-Path-2.18-4.el9.noarch.rpm 558 kB/s | 38 kB 00:00 (149/206): perl-Digest-1.19-4.el9.noarch.rpm 305 kB/s | 29 kB 00:00 (150/206): perl-IO-Socket-IP-0.41-5.el9.noarch. 679 kB/s | 45 kB 00:00 (151/206): perl-Pod-Usage-2.01-4.el9.noarch.rpm 657 kB/s | 43 kB 00:00 (152/206): perl-Socket-2.031-4.el9.x86_64.rpm 839 kB/s | 58 kB 00:00 (153/206): perl-Scalar-List-Utils-1.56-461.el9. 836 kB/s | 77 kB 00:00 (154/206): perl-Term-ANSIColor-5.01-461.el9.noa 668 kB/s | 51 kB 00:00 (155/206): perl-Text-ParseWords-3.30-460.el9.no 283 kB/s | 18 kB 00:00 (156/206): perl-URI-5.09-3.el9.noarch.rpm 1.6 MB/s | 125 kB 00:00 (157/206): fonts-srpm-macros-2.0.5-7.el9.1.noar 428 kB/s | 29 kB 00:00 (158/206): perl-constant-1.33-461.el9.noarch.rp 266 kB/s | 25 kB 00:00 (159/206): ocaml-srpm-macros-6-6.el9.noarch.rpm 134 kB/s | 9.1 kB 00:00 (160/206): perl-libnet-3.13-4.el9.noarch.rpm 2.0 MB/s | 134 kB 00:00 (161/206): perl-Pod-Perldoc-3.28.01-461.el9.noa 1.2 MB/s | 92 kB 00:00 (162/206): patch-2.7.6-16.el9.x86_64.rpm 1.3 MB/s | 130 kB 00:00 (163/206): perl-PathTools-3.78-461.el9.x86_64.r 1.4 MB/s | 92 kB 00:00 (164/206): perl-Carp-1.50-460.el9.noarch.rpm 407 kB/s | 31 kB 00:00 (165/206): perl-Net-SSLeay-1.92-2.el9.x86_64.rp 5.6 MB/s | 392 kB 00:00 (166/206): qt5-srpm-macros-5.15.9-1.el9.noarch. 141 kB/s | 9.1 kB 00:00 (167/206): perl-AutoLoader-5.74-481.el9.noarch. 285 kB/s | 21 kB 00:00 (168/206): kernel-srpm-macros-1.0-13.el9.noarch 148 kB/s | 17 kB 00:00 (169/206): perl-SelectSaver-1.02-481.el9.noarch 166 kB/s | 12 kB 00:00 (170/206): perl-if-0.60.800-481.el9.noarch.rpm 219 kB/s | 14 kB 00:00 (171/206): perl-overloading-0.02-481.el9.noarch 131 kB/s | 13 kB 00:00 (172/206): python-srpm-macros-3.9-53.el9.noarch 217 kB/s | 19 kB 00:00 (173/206): redhat-rpm-config-207-1.el9.noarch.r 584 kB/s | 76 kB 00:00 (174/206): go-srpm-macros-3.2.0-3.el9.noarch.rp 418 kB/s | 28 kB 00:00 (175/206): gdb-minimal-10.2-13.el9.x86_64.rpm 18 MB/s | 3.5 MB 00:00 (176/206): perl-Class-Struct-0.66-481.el9.noarc 182 kB/s | 22 kB 00:00 (177/206): perl-B-1.80-481.el9.x86_64.rpm 1.1 MB/s | 184 kB 00:00 (178/206): perl-File-Basename-2.85-481.el9.noar 243 kB/s | 17 kB 00:00 (179/206): perl-Errno-1.30-481.el9.x86_64.rpm 176 kB/s | 15 kB 00:00 (180/206): perl-File-stat-1.09-481.el9.noarch.r 260 kB/s | 17 kB 00:00 (181/206): perl-FileHandle-2.03-481.el9.noarch. 214 kB/s | 16 kB 00:00 (182/206): perl-HTTP-Tiny-0.076-462.el9.noarch. 878 kB/s | 57 kB 00:00 (183/206): perl-IO-1.43-481.el9.x86_64.rpm 1.4 MB/s | 92 kB 00:00 (184/206): perl-Getopt-Std-1.12-481.el9.noarch. 124 kB/s | 16 kB 00:00 (185/206): perl-IPC-Open3-1.21-481.el9.noarch.r 214 kB/s | 24 kB 00:00 (186/206): perl-Symbol-1.08-481.el9.noarch.rpm 205 kB/s | 14 kB 00:00 (187/206): perl-POSIX-1.94-481.el9.x86_64.rpm 988 kB/s | 98 kB 00:00 (188/206): perl-interpreter-5.32.1-481.el9.x86_ 1.1 MB/s | 73 kB 00:00 (189/206): perl-base-2.27-481.el9.noarch.rpm 192 kB/s | 16 kB 00:00 (190/206): perl-mro-1.23-481.el9.x86_64.rpm 438 kB/s | 29 kB 00:00 (191/206): perl-overload-1.31-481.el9.noarch.rp 366 kB/s | 46 kB 00:00 (192/206): perl-libs-5.32.1-481.el9.x86_64.rpm 10 MB/s | 2.2 MB 00:00 (193/206): pyproject-srpm-macros-1.12.0-1.el9.n 181 kB/s | 14 kB 00:00 (194/206): perl-vars-1.05-481.el9.noarch.rpm 60 kB/s | 13 kB 00:00 (195/206): perl-Fcntl-1.13-481.el9.x86_64.rpm 308 kB/s | 22 kB 00:00 (196/206): debugedit-5.0-5.el9.x86_64.rpm 579 kB/s | 81 kB 00:00 (197/206): perl-subs-1.03-481.el9.noarch.rpm 169 kB/s | 12 kB 00:00 (198/206): rpm-build-4.16.1.3-29.el9.x86_64.rpm 906 kB/s | 72 kB 00:00 (199/206): ansible-srpm-macros-1-12.el9.noarch. 97 kB/s | 21 kB 00:00 (200/206): epel-rpm-macros-9-14.el9.noarch.rpm 85 kB/s | 15 kB 00:00 (201/206): forge-srpm-macros-0.3.1-1.el9.noarch 100 kB/s | 19 kB 00:00 (202/206): fpc-srpm-macros-1.3-7.el9.noarch.rpm 154 kB/s | 7.5 kB 00:00 (203/206): go-srpm-macros-epel-3.3.0.5-1.el9.no 379 kB/s | 27 kB 00:00 (204/206): qt6-srpm-macros-6.6.2-1.el9.noarch.r 167 kB/s | 8.7 kB 00:00 (205/206): rpmautospec-rpm-macros-0.6.3-1.el9.n 187 kB/s | 9.9 kB 00:00 (206/206): rust-srpm-macros-epel-26.3-1.el9.noa 199 kB/s | 10 kB 00:00 -------------------------------------------------------------------------------- Total 9.0 MB/s | 68 MB 00:07 Red Hat Enterprise Linux - BaseOS 3.5 MB/s | 3.6 kB 00:00 Importing GPG key 0xFD431D51: Userid : "Red Hat, Inc. (release key 2) " Fingerprint: 567E 347A D004 4ADE 55BA 8A5F 199E 2F91 FD43 1D51 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat9-release Key imported successfully Importing GPG key 0x5A6340B3: Userid : "Red Hat, Inc. (auxiliary key 3) " Fingerprint: 7E46 2425 8C40 6535 D56D 6F13 5054 E4A4 5A63 40B3 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat9-release Key imported successfully Extra Packages for Enterprise Linux 9 - x86_64 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x3228467C: Userid : "Fedora (epel9) " Fingerprint: FF8A D134 4597 106E CE81 3B91 8A38 72BF 3228 467C From : /usr/share/distribution-gpg-keys/epel/RPM-GPG-KEY-EPEL-9 Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.16-2.el9.x86_64 1/1 Preparing : 1/1 Installing : libgcc-11.4.1-3.el9.x86_64 1/206 Running scriptlet: libgcc-11.4.1-3.el9.x86_64 1/206 Installing : crypto-policies-20240202-1.git283706d.el9.noarch 2/206 Running scriptlet: crypto-policies-20240202-1.git283706d.el9.noarch 2/206 Installing : rust-srpm-macros-17-4.el9.noarch 3/206 Installing : redhat-release-9.4-0.4.el9.x86_64 4/206 Installing : setup-2.13.7-10.el9.noarch 5/206 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.13.7-10.el9.noarch 5/206 Installing : filesystem-3.16-2.el9.x86_64 6/206 Installing : basesystem-11-13.el9.noarch 7/206 Installing : rust-srpm-macros-epel-26.3-1.el9.noarch 8/206 Installing : qt6-srpm-macros-6.6.2-1.el9.noarch 9/206 Installing : fpc-srpm-macros-1.3-7.el9.noarch 10/206 Installing : ansible-srpm-macros-1-12.el9.noarch 11/206 Installing : qt5-srpm-macros-5.15.9-1.el9.noarch 12/206 Installing : ocaml-srpm-macros-6-6.el9.noarch 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: go-srpm-macros-epel-3.3.0.5-1.el9.noarch 203/206 Installing : epel-rpm-macros-9-14.el9.noarch 204/206 Installing : util-linux-2.37.4-18.el9.x86_64 205/206 Installing : which-2.21-29.el9.x86_64 206/206 Running scriptlet: filesystem-3.16-2.el9.x86_64 206/206 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-90.1.el9_2.no 206/206 Running scriptlet: rpm-4.16.1.3-29.el9.x86_64 206/206 Running scriptlet: which-2.21-29.el9.x86_64 206/206 Verifying : basesystem-11-13.el9.noarch 1/206 Verifying : bzip2-1.0.8-8.el9.x86_64 2/206 Verifying : bzip2-libs-1.0.8-8.el9.x86_64 3/206 Verifying : cpio-2.13-16.el9.x86_64 4/206 Verifying : cracklib-2.9.6-27.el9.x86_64 5/206 Verifying : ed-1.14.2-12.el9.x86_64 6/206 Verifying : filesystem-3.16-2.el9.x86_64 7/206 Verifying : grep-3.6-5.el9.x86_64 8/206 Verifying : groff-base-1.22.4-10.el9.x86_64 9/206 Verifying : info-6.7-15.el9.x86_64 10/206 Verifying : libattr-2.5.1-3.el9.x86_64 11/206 Verifying : libbrotli-1.0.9-6.el9.x86_64 12/206 Verifying : libcap-ng-0.8.2-7.el9.x86_64 13/206 Verifying : libdb-5.3.28-53.el9.x86_64 14/206 Verifying : libevent-2.1.12-6.el9.x86_64 15/206 Verifying : libgpg-error-1.42-5.el9.x86_64 16/206 Verifying : libidn2-2.3.0-7.el9.x86_64 17/206 Verifying : libpsl-0.21.1-5.el9.x86_64 18/206 Verifying : libpwquality-1.4.4-8.el9.x86_64 19/206 Verifying : libsigsegv-2.13-4.el9.x86_64 20/206 Verifying : libunistring-0.9.10-15.el9.x86_64 21/206 Verifying : libutempter-1.2.1-6.el9.x86_64 22/206 Verifying : libverto-0.3.2-3.el9.x86_64 23/206 Verifying : libxcrypt-4.4.18-3.el9.x86_64 24/206 Verifying : libzstd-1.5.1-2.el9.x86_64 25/206 Verifying : lz4-libs-1.9.3-5.el9.x86_64 26/206 Verifying : mpfr-4.1.0-7.el9.x86_64 27/206 Verifying : pcre-8.44-3.el9.3.x86_64 28/206 Verifying : popt-1.18-8.el9.x86_64 29/206 Verifying : publicsuffix-list-dafsa-20210518-3.el9.noarch 30/206 Verifying : readline-8.1-4.el9.x86_64 31/206 Verifying : sed-4.8-9.el9.x86_64 32/206 Verifying : unzip-6.0-56.el9.x86_64 33/206 Verifying : cracklib-dicts-2.9.6-27.el9.x86_64 34/206 Verifying : diffutils-3.7-12.el9.x86_64 35/206 Verifying : gawk-5.1.0-6.el9.x86_64 36/206 Verifying : gdbm-libs-1:1.19-4.el9.x86_64 37/206 Verifying : xz-5.2.5-8.el9_0.x86_64 38/206 Verifying : xz-libs-5.2.5-8.el9_0.x86_64 39/206 Verifying : zstd-1.5.1-2.el9.x86_64 40/206 Verifying : cyrus-sasl-lib-2.1.27-21.el9.x86_64 41/206 Verifying : gzip-1.12-1.el9.x86_64 42/206 Verifying : libtasn1-4.16.0-8.el9_1.x86_64 43/206 Verifying : tar-2:1.34-6.el9_1.x86_64 44/206 Verifying : ca-certificates-2023.2.60_v7.0.306-90.1.el9_2.no 45/206 Verifying : keyutils-libs-1.6.3-1.el9.x86_64 46/206 Verifying : libarchive-3.5.3-4.el9.x86_64 47/206 Verifying : libcap-2.48-9.el9_2.x86_64 48/206 Verifying : libeconf-0.4.1-3.el9_2.x86_64 49/206 Verifying : libgcrypt-1.10.0-10.el9_2.x86_64 50/206 Verifying : libpkgconf-1.7.3-10.el9.x86_64 51/206 Verifying : pkgconf-1.7.3-10.el9.x86_64 52/206 Verifying : pkgconf-m4-1.7.3-10.el9.noarch 53/206 Verifying : pkgconf-pkg-config-1.7.3-10.el9.x86_64 54/206 Verifying : zip-3.0-35.el9.x86_64 55/206 Verifying : alternatives-1.24-1.el9.x86_64 56/206 Verifying : findutils-1:4.8.0-6.el9.x86_64 57/206 Verifying : gmp-1:6.2.0-13.el9.x86_64 58/206 Verifying : krb5-libs-1.21.1-1.el9.x86_64 59/206 Verifying : libffi-3.4.2-8.el9.x86_64 60/206 Verifying : lua-libs-5.4.4-4.el9.x86_64 61/206 Verifying : ncurses-6.2-10.20210508.el9.x86_64 62/206 Verifying : ncurses-base-6.2-10.20210508.el9.noarch 63/206 Verifying : ncurses-libs-6.2-10.20210508.el9.x86_64 64/206 Verifying : shadow-utils-2:4.9-8.el9.x86_64 65/206 Verifying : which-2.21-29.el9.x86_64 66/206 Verifying : zlib-1.2.11-40.el9.x86_64 67/206 Verifying : audit-libs-3.1.2-2.el9.x86_64 68/206 Verifying : bash-5.1.8-9.el9.x86_64 69/206 Verifying : binutils-2.35.2-43.el9.x86_64 70/206 Verifying : binutils-gold-2.35.2-43.el9.x86_64 71/206 Verifying : coreutils-8.32-35.el9.x86_64 72/206 Verifying : coreutils-common-8.32-35.el9.x86_64 73/206 Verifying : curl-7.76.1-29.el9_4.x86_64 74/206 Verifying : elfutils-0.190-2.el9.x86_64 75/206 Verifying : elfutils-default-yama-scope-0.190-2.el9.noarch 76/206 Verifying : elfutils-libs-0.190-2.el9.x86_64 77/206 Verifying : file-5.39-16.el9.x86_64 78/206 Verifying : file-libs-5.39-16.el9.x86_64 79/206 Verifying : libacl-2.3.1-4.el9.x86_64 80/206 Verifying : libblkid-2.37.4-18.el9.x86_64 81/206 Verifying : libfdisk-2.37.4-18.el9.x86_64 82/206 Verifying : libgcc-11.4.1-3.el9.x86_64 83/206 Verifying : libgomp-11.4.1-3.el9.x86_64 84/206 Verifying : libmount-2.37.4-18.el9.x86_64 85/206 Verifying : libselinux-3.6-1.el9.x86_64 86/206 Verifying : libsemanage-3.6-1.el9.x86_64 87/206 Verifying : libsepol-3.6-1.el9.x86_64 88/206 Verifying : libsmartcols-2.37.4-18.el9.x86_64 89/206 Verifying : libstdc++-11.4.1-3.el9.x86_64 90/206 Verifying : libuuid-2.37.4-18.el9.x86_64 91/206 Verifying : openldap-2.6.6-3.el9.x86_64 92/206 Verifying : openssl-1:3.0.7-27.el9.x86_64 93/206 Verifying : openssl-fips-provider-3.0.7-2.el9.x86_64 94/206 Verifying : openssl-libs-1:3.0.7-27.el9.x86_64 95/206 Verifying : p11-kit-0.25.3-2.el9.x86_64 96/206 Verifying : p11-kit-trust-0.25.3-2.el9.x86_64 97/206 Verifying : pam-1.5.1-19.el9.x86_64 98/206 Verifying : pcre2-10.40-5.el9.x86_64 99/206 Verifying : rpm-4.16.1.3-29.el9.x86_64 100/206 Verifying : rpm-build-libs-4.16.1.3-29.el9.x86_64 101/206 Verifying : rpm-libs-4.16.1.3-29.el9.x86_64 102/206 Verifying : setup-2.13.7-10.el9.noarch 103/206 Verifying : sqlite-libs-3.34.1-7.el9_3.x86_64 104/206 Verifying : systemd-libs-252-32.el9_4.x86_64 105/206 Verifying : tzdata-2024a-1.el9.noarch 106/206 Verifying : util-linux-2.37.4-18.el9.x86_64 107/206 Verifying : util-linux-core-2.37.4-18.el9.x86_64 108/206 Verifying : crypto-policies-20240202-1.git283706d.el9.noarch 109/206 Verifying : elfutils-debuginfod-client-0.190-2.el9.x86_64 110/206 Verifying : elfutils-libelf-0.190-2.el9.x86_64 111/206 Verifying : libcom_err-1.46.5-5.el9.x86_64 112/206 Verifying : libcurl-7.76.1-29.el9_4.x86_64 113/206 Verifying : libssh-0.10.4-13.el9.x86_64 114/206 Verifying : libssh-config-0.10.4-13.el9.noarch 115/206 Verifying : pcre2-syntax-10.40-5.el9.noarch 116/206 Verifying : redhat-release-9.4-0.4.el9.x86_64 117/206 Verifying : libxml2-2.9.13-6.el9_4.x86_64 118/206 Verifying : glibc-2.34-100.el9_4.2.x86_64 119/206 Verifying : glibc-common-2.34-100.el9_4.2.x86_64 120/206 Verifying : glibc-gconv-extra-2.34-100.el9_4.2.x86_64 121/206 Verifying : glibc-minimal-langpack-2.34-100.el9_4.2.x86_64 122/206 Verifying : libnghttp2-1.43.0-5.el9_4.3.x86_64 123/206 Verifying : ghc-srpm-macros-1.5.0-6.el9.noarch 124/206 Verifying : lua-srpm-macros-1-6.el9.noarch 125/206 Verifying : perl-Data-Dumper-2.174-462.el9.x86_64 126/206 Verifying : perl-Digest-MD5-2.58-4.el9.x86_64 127/206 Verifying : perl-Encode-4:3.08-462.el9.x86_64 128/206 Verifying : perl-IO-Socket-SSL-2.073-1.el9.noarch 129/206 Verifying : perl-Mozilla-CA-20200520-6.el9.noarch 130/206 Verifying : perl-Pod-Simple-1:3.42-4.el9.noarch 131/206 Verifying : perl-Term-Cap-1.17-460.el9.noarch 132/206 Verifying : perl-Time-Local-2:1.300-7.el9.noarch 133/206 Verifying : rust-srpm-macros-17-4.el9.noarch 134/206 Verifying : perl-Pod-Escapes-1:1.07-460.el9.noarch 135/206 Verifying : perl-Storable-1:3.21-460.el9.x86_64 136/206 Verifying : perl-podlators-1:4.14-460.el9.noarch 137/206 Verifying : dwz-0.14-3.el9.x86_64 138/206 Verifying : perl-Exporter-5.74-461.el9.noarch 139/206 Verifying : perl-File-Temp-1:0.231.100-4.el9.noarch 140/206 Verifying : perl-Getopt-Long-1:2.52-4.el9.noarch 141/206 Verifying : perl-MIME-Base64-3.16-4.el9.x86_64 142/206 Verifying : perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch 143/206 Verifying : perl-parent-1:0.238-460.el9.noarch 144/206 Verifying : perl-srpm-macros-1-41.el9.noarch 145/206 Verifying : efi-srpm-macros-6-2.el9_0.noarch 146/206 Verifying : openblas-srpm-macros-2-11.el9.noarch 147/206 Verifying : perl-Digest-1.19-4.el9.noarch 148/206 Verifying : perl-File-Path-2.18-4.el9.noarch 149/206 Verifying : perl-IO-Socket-IP-0.41-5.el9.noarch 150/206 Verifying : perl-Pod-Usage-4:2.01-4.el9.noarch 151/206 Verifying : perl-Scalar-List-Utils-4:1.56-461.el9.x86_64 152/206 Verifying : perl-Socket-4:2.031-4.el9.x86_64 153/206 Verifying : perl-Term-ANSIColor-5.01-461.el9.noarch 154/206 Verifying : perl-Text-ParseWords-3.30-460.el9.noarch 155/206 Verifying : perl-URI-5.09-3.el9.noarch 156/206 Verifying : perl-constant-1.33-461.el9.noarch 157/206 Verifying : fonts-srpm-macros-1:2.0.5-7.el9.1.noarch 158/206 Verifying : ocaml-srpm-macros-6-6.el9.noarch 159/206 Verifying : patch-2.7.6-16.el9.x86_64 160/206 Verifying : perl-Pod-Perldoc-3.28.01-461.el9.noarch 161/206 Verifying : perl-libnet-3.13-4.el9.noarch 162/206 Verifying : perl-Carp-1.50-460.el9.noarch 163/206 Verifying : perl-PathTools-3.78-461.el9.x86_64 164/206 Verifying : perl-Net-SSLeay-1.92-2.el9.x86_64 165/206 Verifying : kernel-srpm-macros-1.0-13.el9.noarch 166/206 Verifying : qt5-srpm-macros-5.15.9-1.el9.noarch 167/206 Verifying : perl-AutoLoader-5.74-481.el9.noarch 168/206 Verifying : perl-SelectSaver-1.02-481.el9.noarch 169/206 Verifying : perl-if-0.60.800-481.el9.noarch 170/206 Verifying : perl-overloading-0.02-481.el9.noarch 171/206 Verifying : python-srpm-macros-3.9-53.el9.noarch 172/206 Verifying : redhat-rpm-config-207-1.el9.noarch 173/206 Verifying : gdb-minimal-10.2-13.el9.x86_64 174/206 Verifying : go-srpm-macros-3.2.0-3.el9.noarch 175/206 Verifying : perl-B-1.80-481.el9.x86_64 176/206 Verifying : perl-Class-Struct-0.66-481.el9.noarch 177/206 Verifying : perl-Errno-1.30-481.el9.x86_64 178/206 Verifying : perl-File-Basename-2.85-481.el9.noarch 179/206 Verifying : perl-File-stat-1.09-481.el9.noarch 180/206 Verifying : perl-FileHandle-2.03-481.el9.noarch 181/206 Verifying : perl-Getopt-Std-1.12-481.el9.noarch 182/206 Verifying : perl-HTTP-Tiny-0.076-462.el9.noarch 183/206 Verifying : perl-IO-1.43-481.el9.x86_64 184/206 Verifying : perl-IPC-Open3-1.21-481.el9.noarch 185/206 Verifying : perl-POSIX-1.94-481.el9.x86_64 186/206 Verifying : perl-Symbol-1.08-481.el9.noarch 187/206 Verifying : perl-base-2.27-481.el9.noarch 188/206 Verifying : perl-interpreter-4:5.32.1-481.el9.x86_64 189/206 Verifying : perl-libs-4:5.32.1-481.el9.x86_64 190/206 Verifying : perl-mro-1.23-481.el9.x86_64 191/206 Verifying : perl-overload-1.31-481.el9.noarch 192/206 Verifying : perl-vars-1.05-481.el9.noarch 193/206 Verifying : pyproject-srpm-macros-1.12.0-1.el9.noarch 194/206 Verifying : debugedit-5.0-5.el9.x86_64 195/206 Verifying : perl-Fcntl-1.13-481.el9.x86_64 196/206 Verifying : perl-subs-1.03-481.el9.noarch 197/206 Verifying : rpm-build-4.16.1.3-29.el9.x86_64 198/206 Verifying : ansible-srpm-macros-1-12.el9.noarch 199/206 Verifying : epel-rpm-macros-9-14.el9.noarch 200/206 Verifying : forge-srpm-macros-0.3.1-1.el9.noarch 201/206 Verifying : fpc-srpm-macros-1.3-7.el9.noarch 202/206 Verifying : go-srpm-macros-epel-3.3.0.5-1.el9.noarch 203/206 Verifying : qt6-srpm-macros-6.6.2-1.el9.noarch 204/206 Verifying : rpmautospec-rpm-macros-0.6.3-1.el9.noarch 205/206 Verifying : rust-srpm-macros-epel-26.3-1.el9.noarch 206/206 Installed products updated. Installed: alternatives-1.24-1.el9.x86_64 ansible-srpm-macros-1-12.el9.noarch audit-libs-3.1.2-2.el9.x86_64 basesystem-11-13.el9.noarch bash-5.1.8-9.el9.x86_64 binutils-2.35.2-43.el9.x86_64 binutils-gold-2.35.2-43.el9.x86_64 bzip2-1.0.8-8.el9.x86_64 bzip2-libs-1.0.8-8.el9.x86_64 ca-certificates-2023.2.60_v7.0.306-90.1.el9_2.noarch coreutils-8.32-35.el9.x86_64 coreutils-common-8.32-35.el9.x86_64 cpio-2.13-16.el9.x86_64 cracklib-2.9.6-27.el9.x86_64 cracklib-dicts-2.9.6-27.el9.x86_64 crypto-policies-20240202-1.git283706d.el9.noarch curl-7.76.1-29.el9_4.x86_64 cyrus-sasl-lib-2.1.27-21.el9.x86_64 debugedit-5.0-5.el9.x86_64 diffutils-3.7-12.el9.x86_64 dwz-0.14-3.el9.x86_64 ed-1.14.2-12.el9.x86_64 efi-srpm-macros-6-2.el9_0.noarch elfutils-0.190-2.el9.x86_64 elfutils-debuginfod-client-0.190-2.el9.x86_64 elfutils-default-yama-scope-0.190-2.el9.noarch elfutils-libelf-0.190-2.el9.x86_64 elfutils-libs-0.190-2.el9.x86_64 epel-rpm-macros-9-14.el9.noarch file-5.39-16.el9.x86_64 file-libs-5.39-16.el9.x86_64 filesystem-3.16-2.el9.x86_64 findutils-1:4.8.0-6.el9.x86_64 fonts-srpm-macros-1:2.0.5-7.el9.1.noarch forge-srpm-macros-0.3.1-1.el9.noarch fpc-srpm-macros-1.3-7.el9.noarch gawk-5.1.0-6.el9.x86_64 gdb-minimal-10.2-13.el9.x86_64 gdbm-libs-1:1.19-4.el9.x86_64 ghc-srpm-macros-1.5.0-6.el9.noarch glibc-2.34-100.el9_4.2.x86_64 glibc-common-2.34-100.el9_4.2.x86_64 glibc-gconv-extra-2.34-100.el9_4.2.x86_64 glibc-minimal-langpack-2.34-100.el9_4.2.x86_64 gmp-1:6.2.0-13.el9.x86_64 go-srpm-macros-3.2.0-3.el9.noarch go-srpm-macros-epel-3.3.0.5-1.el9.noarch grep-3.6-5.el9.x86_64 groff-base-1.22.4-10.el9.x86_64 gzip-1.12-1.el9.x86_64 info-6.7-15.el9.x86_64 kernel-srpm-macros-1.0-13.el9.noarch keyutils-libs-1.6.3-1.el9.x86_64 krb5-libs-1.21.1-1.el9.x86_64 libacl-2.3.1-4.el9.x86_64 libarchive-3.5.3-4.el9.x86_64 libattr-2.5.1-3.el9.x86_64 libblkid-2.37.4-18.el9.x86_64 libbrotli-1.0.9-6.el9.x86_64 libcap-2.48-9.el9_2.x86_64 libcap-ng-0.8.2-7.el9.x86_64 libcom_err-1.46.5-5.el9.x86_64 libcurl-7.76.1-29.el9_4.x86_64 libdb-5.3.28-53.el9.x86_64 libeconf-0.4.1-3.el9_2.x86_64 libevent-2.1.12-6.el9.x86_64 libfdisk-2.37.4-18.el9.x86_64 libffi-3.4.2-8.el9.x86_64 libgcc-11.4.1-3.el9.x86_64 libgcrypt-1.10.0-10.el9_2.x86_64 libgomp-11.4.1-3.el9.x86_64 libgpg-error-1.42-5.el9.x86_64 libidn2-2.3.0-7.el9.x86_64 libmount-2.37.4-18.el9.x86_64 libnghttp2-1.43.0-5.el9_4.3.x86_64 libpkgconf-1.7.3-10.el9.x86_64 libpsl-0.21.1-5.el9.x86_64 libpwquality-1.4.4-8.el9.x86_64 libselinux-3.6-1.el9.x86_64 libsemanage-3.6-1.el9.x86_64 libsepol-3.6-1.el9.x86_64 libsigsegv-2.13-4.el9.x86_64 libsmartcols-2.37.4-18.el9.x86_64 libssh-0.10.4-13.el9.x86_64 libssh-config-0.10.4-13.el9.noarch libstdc++-11.4.1-3.el9.x86_64 libtasn1-4.16.0-8.el9_1.x86_64 libunistring-0.9.10-15.el9.x86_64 libutempter-1.2.1-6.el9.x86_64 libuuid-2.37.4-18.el9.x86_64 libverto-0.3.2-3.el9.x86_64 libxcrypt-4.4.18-3.el9.x86_64 libxml2-2.9.13-6.el9_4.x86_64 libzstd-1.5.1-2.el9.x86_64 lua-libs-5.4.4-4.el9.x86_64 lua-srpm-macros-1-6.el9.noarch lz4-libs-1.9.3-5.el9.x86_64 mpfr-4.1.0-7.el9.x86_64 ncurses-6.2-10.20210508.el9.x86_64 ncurses-base-6.2-10.20210508.el9.noarch ncurses-libs-6.2-10.20210508.el9.x86_64 ocaml-srpm-macros-6-6.el9.noarch openblas-srpm-macros-2-11.el9.noarch openldap-2.6.6-3.el9.x86_64 openssl-1:3.0.7-27.el9.x86_64 openssl-fips-provider-3.0.7-2.el9.x86_64 openssl-libs-1:3.0.7-27.el9.x86_64 p11-kit-0.25.3-2.el9.x86_64 p11-kit-trust-0.25.3-2.el9.x86_64 pam-1.5.1-19.el9.x86_64 patch-2.7.6-16.el9.x86_64 pcre-8.44-3.el9.3.x86_64 pcre2-10.40-5.el9.x86_64 pcre2-syntax-10.40-5.el9.noarch perl-AutoLoader-5.74-481.el9.noarch perl-B-1.80-481.el9.x86_64 perl-Carp-1.50-460.el9.noarch perl-Class-Struct-0.66-481.el9.noarch perl-Data-Dumper-2.174-462.el9.x86_64 perl-Digest-1.19-4.el9.noarch perl-Digest-MD5-2.58-4.el9.x86_64 perl-Encode-4:3.08-462.el9.x86_64 perl-Errno-1.30-481.el9.x86_64 perl-Exporter-5.74-461.el9.noarch perl-Fcntl-1.13-481.el9.x86_64 perl-File-Basename-2.85-481.el9.noarch perl-File-Path-2.18-4.el9.noarch perl-File-Temp-1:0.231.100-4.el9.noarch perl-File-stat-1.09-481.el9.noarch perl-FileHandle-2.03-481.el9.noarch perl-Getopt-Long-1:2.52-4.el9.noarch perl-Getopt-Std-1.12-481.el9.noarch perl-HTTP-Tiny-0.076-462.el9.noarch perl-IO-1.43-481.el9.x86_64 perl-IO-Socket-IP-0.41-5.el9.noarch perl-IO-Socket-SSL-2.073-1.el9.noarch perl-IPC-Open3-1.21-481.el9.noarch perl-MIME-Base64-3.16-4.el9.x86_64 perl-Mozilla-CA-20200520-6.el9.noarch perl-Net-SSLeay-1.92-2.el9.x86_64 perl-POSIX-1.94-481.el9.x86_64 perl-PathTools-3.78-461.el9.x86_64 perl-Pod-Escapes-1:1.07-460.el9.noarch perl-Pod-Perldoc-3.28.01-461.el9.noarch perl-Pod-Simple-1:3.42-4.el9.noarch perl-Pod-Usage-4:2.01-4.el9.noarch perl-Scalar-List-Utils-4:1.56-461.el9.x86_64 perl-SelectSaver-1.02-481.el9.noarch perl-Socket-4:2.031-4.el9.x86_64 perl-Storable-1:3.21-460.el9.x86_64 perl-Symbol-1.08-481.el9.noarch perl-Term-ANSIColor-5.01-461.el9.noarch perl-Term-Cap-1.17-460.el9.noarch perl-Text-ParseWords-3.30-460.el9.noarch perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch perl-Time-Local-2:1.300-7.el9.noarch perl-URI-5.09-3.el9.noarch perl-base-2.27-481.el9.noarch perl-constant-1.33-461.el9.noarch perl-if-0.60.800-481.el9.noarch perl-interpreter-4:5.32.1-481.el9.x86_64 perl-libnet-3.13-4.el9.noarch perl-libs-4:5.32.1-481.el9.x86_64 perl-mro-1.23-481.el9.x86_64 perl-overload-1.31-481.el9.noarch perl-overloading-0.02-481.el9.noarch perl-parent-1:0.238-460.el9.noarch perl-podlators-1:4.14-460.el9.noarch perl-srpm-macros-1-41.el9.noarch perl-subs-1.03-481.el9.noarch perl-vars-1.05-481.el9.noarch pkgconf-1.7.3-10.el9.x86_64 pkgconf-m4-1.7.3-10.el9.noarch pkgconf-pkg-config-1.7.3-10.el9.x86_64 popt-1.18-8.el9.x86_64 publicsuffix-list-dafsa-20210518-3.el9.noarch pyproject-srpm-macros-1.12.0-1.el9.noarch python-srpm-macros-3.9-53.el9.noarch qt5-srpm-macros-5.15.9-1.el9.noarch qt6-srpm-macros-6.6.2-1.el9.noarch readline-8.1-4.el9.x86_64 redhat-release-9.4-0.4.el9.x86_64 redhat-rpm-config-207-1.el9.noarch rpm-4.16.1.3-29.el9.x86_64 rpm-build-4.16.1.3-29.el9.x86_64 rpm-build-libs-4.16.1.3-29.el9.x86_64 rpm-libs-4.16.1.3-29.el9.x86_64 rpmautospec-rpm-macros-0.6.3-1.el9.noarch rust-srpm-macros-17-4.el9.noarch rust-srpm-macros-epel-26.3-1.el9.noarch sed-4.8-9.el9.x86_64 setup-2.13.7-10.el9.noarch shadow-utils-2:4.9-8.el9.x86_64 sqlite-libs-3.34.1-7.el9_3.x86_64 systemd-libs-252-32.el9_4.x86_64 tar-2:1.34-6.el9_1.x86_64 tzdata-2024a-1.el9.noarch unzip-6.0-56.el9.x86_64 util-linux-2.37.4-18.el9.x86_64 util-linux-core-2.37.4-18.el9.x86_64 which-2.21-29.el9.x86_64 xz-5.2.5-8.el9_0.x86_64 xz-libs-5.2.5-8.el9_0.x86_64 zip-3.0-35.el9.x86_64 zlib-1.2.11-40.el9.x86_64 zstd-1.5.1-2.el9.x86_64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.24-1.el9.x86_64 ansible-srpm-macros-1-12.el9.noarch audit-libs-3.1.2-2.el9.x86_64 basesystem-11-13.el9.noarch bash-5.1.8-9.el9.x86_64 binutils-2.35.2-43.el9.x86_64 binutils-gold-2.35.2-43.el9.x86_64 bzip2-1.0.8-8.el9.x86_64 bzip2-libs-1.0.8-8.el9.x86_64 ca-certificates-2023.2.60_v7.0.306-90.1.el9_2.noarch coreutils-8.32-35.el9.x86_64 coreutils-common-8.32-35.el9.x86_64 cpio-2.13-16.el9.x86_64 cracklib-2.9.6-27.el9.x86_64 cracklib-dicts-2.9.6-27.el9.x86_64 crypto-policies-20240202-1.git283706d.el9.noarch curl-7.76.1-29.el9_4.x86_64 cyrus-sasl-lib-2.1.27-21.el9.x86_64 debugedit-5.0-5.el9.x86_64 diffutils-3.7-12.el9.x86_64 dwz-0.14-3.el9.x86_64 ed-1.14.2-12.el9.x86_64 efi-srpm-macros-6-2.el9_0.noarch elfutils-0.190-2.el9.x86_64 elfutils-debuginfod-client-0.190-2.el9.x86_64 elfutils-default-yama-scope-0.190-2.el9.noarch elfutils-libelf-0.190-2.el9.x86_64 elfutils-libs-0.190-2.el9.x86_64 epel-rpm-macros-9-14.el9.noarch file-5.39-16.el9.x86_64 file-libs-5.39-16.el9.x86_64 filesystem-3.16-2.el9.x86_64 findutils-4.8.0-6.el9.x86_64 fonts-srpm-macros-2.0.5-7.el9.1.noarch forge-srpm-macros-0.3.1-1.el9.noarch fpc-srpm-macros-1.3-7.el9.noarch gawk-5.1.0-6.el9.x86_64 gdb-minimal-10.2-13.el9.x86_64 gdbm-libs-1.19-4.el9.x86_64 ghc-srpm-macros-1.5.0-6.el9.noarch glibc-2.34-100.el9_4.2.x86_64 glibc-common-2.34-100.el9_4.2.x86_64 glibc-gconv-extra-2.34-100.el9_4.2.x86_64 glibc-minimal-langpack-2.34-100.el9_4.2.x86_64 gmp-6.2.0-13.el9.x86_64 go-srpm-macros-3.2.0-3.el9.noarch go-srpm-macros-epel-3.3.0.5-1.el9.noarch gpg-pubkey-3228467c-613798eb gpg-pubkey-5a6340b3-6229229e gpg-pubkey-fd431d51-4ae0493b grep-3.6-5.el9.x86_64 groff-base-1.22.4-10.el9.x86_64 gzip-1.12-1.el9.x86_64 info-6.7-15.el9.x86_64 kernel-srpm-macros-1.0-13.el9.noarch keyutils-libs-1.6.3-1.el9.x86_64 krb5-libs-1.21.1-1.el9.x86_64 libacl-2.3.1-4.el9.x86_64 libarchive-3.5.3-4.el9.x86_64 libattr-2.5.1-3.el9.x86_64 libblkid-2.37.4-18.el9.x86_64 libbrotli-1.0.9-6.el9.x86_64 libcap-2.48-9.el9_2.x86_64 libcap-ng-0.8.2-7.el9.x86_64 libcom_err-1.46.5-5.el9.x86_64 libcurl-7.76.1-29.el9_4.x86_64 libdb-5.3.28-53.el9.x86_64 libeconf-0.4.1-3.el9_2.x86_64 libevent-2.1.12-6.el9.x86_64 libfdisk-2.37.4-18.el9.x86_64 libffi-3.4.2-8.el9.x86_64 libgcc-11.4.1-3.el9.x86_64 libgcrypt-1.10.0-10.el9_2.x86_64 libgomp-11.4.1-3.el9.x86_64 libgpg-error-1.42-5.el9.x86_64 libidn2-2.3.0-7.el9.x86_64 libmount-2.37.4-18.el9.x86_64 libnghttp2-1.43.0-5.el9_4.3.x86_64 libpkgconf-1.7.3-10.el9.x86_64 libpsl-0.21.1-5.el9.x86_64 libpwquality-1.4.4-8.el9.x86_64 libselinux-3.6-1.el9.x86_64 libsemanage-3.6-1.el9.x86_64 libsepol-3.6-1.el9.x86_64 libsigsegv-2.13-4.el9.x86_64 libsmartcols-2.37.4-18.el9.x86_64 libssh-0.10.4-13.el9.x86_64 libssh-config-0.10.4-13.el9.noarch libstdc++-11.4.1-3.el9.x86_64 libtasn1-4.16.0-8.el9_1.x86_64 libunistring-0.9.10-15.el9.x86_64 libutempter-1.2.1-6.el9.x86_64 libuuid-2.37.4-18.el9.x86_64 libverto-0.3.2-3.el9.x86_64 libxcrypt-4.4.18-3.el9.x86_64 libxml2-2.9.13-6.el9_4.x86_64 libzstd-1.5.1-2.el9.x86_64 lua-libs-5.4.4-4.el9.x86_64 lua-srpm-macros-1-6.el9.noarch lz4-libs-1.9.3-5.el9.x86_64 mpfr-4.1.0-7.el9.x86_64 ncurses-6.2-10.20210508.el9.x86_64 ncurses-base-6.2-10.20210508.el9.noarch ncurses-libs-6.2-10.20210508.el9.x86_64 ocaml-srpm-macros-6-6.el9.noarch openblas-srpm-macros-2-11.el9.noarch openldap-2.6.6-3.el9.x86_64 openssl-3.0.7-27.el9.x86_64 openssl-fips-provider-3.0.7-2.el9.x86_64 openssl-libs-3.0.7-27.el9.x86_64 p11-kit-0.25.3-2.el9.x86_64 p11-kit-trust-0.25.3-2.el9.x86_64 pam-1.5.1-19.el9.x86_64 patch-2.7.6-16.el9.x86_64 pcre-8.44-3.el9.3.x86_64 pcre2-10.40-5.el9.x86_64 pcre2-syntax-10.40-5.el9.noarch perl-AutoLoader-5.74-481.el9.noarch perl-B-1.80-481.el9.x86_64 perl-Carp-1.50-460.el9.noarch perl-Class-Struct-0.66-481.el9.noarch perl-Data-Dumper-2.174-462.el9.x86_64 perl-Digest-1.19-4.el9.noarch perl-Digest-MD5-2.58-4.el9.x86_64 perl-Encode-3.08-462.el9.x86_64 perl-Errno-1.30-481.el9.x86_64 perl-Exporter-5.74-461.el9.noarch perl-Fcntl-1.13-481.el9.x86_64 perl-File-Basename-2.85-481.el9.noarch perl-File-Path-2.18-4.el9.noarch perl-File-Temp-0.231.100-4.el9.noarch perl-File-stat-1.09-481.el9.noarch perl-FileHandle-2.03-481.el9.noarch perl-Getopt-Long-2.52-4.el9.noarch perl-Getopt-Std-1.12-481.el9.noarch perl-HTTP-Tiny-0.076-462.el9.noarch perl-IO-1.43-481.el9.x86_64 perl-IO-Socket-IP-0.41-5.el9.noarch perl-IO-Socket-SSL-2.073-1.el9.noarch perl-IPC-Open3-1.21-481.el9.noarch perl-MIME-Base64-3.16-4.el9.x86_64 perl-Mozilla-CA-20200520-6.el9.noarch perl-Net-SSLeay-1.92-2.el9.x86_64 perl-POSIX-1.94-481.el9.x86_64 perl-PathTools-3.78-461.el9.x86_64 perl-Pod-Escapes-1.07-460.el9.noarch perl-Pod-Perldoc-3.28.01-461.el9.noarch perl-Pod-Simple-3.42-4.el9.noarch perl-Pod-Usage-2.01-4.el9.noarch perl-Scalar-List-Utils-1.56-461.el9.x86_64 perl-SelectSaver-1.02-481.el9.noarch perl-Socket-2.031-4.el9.x86_64 perl-Storable-3.21-460.el9.x86_64 perl-Symbol-1.08-481.el9.noarch perl-Term-ANSIColor-5.01-461.el9.noarch perl-Term-Cap-1.17-460.el9.noarch perl-Text-ParseWords-3.30-460.el9.noarch perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch perl-Time-Local-1.300-7.el9.noarch perl-URI-5.09-3.el9.noarch perl-base-2.27-481.el9.noarch perl-constant-1.33-461.el9.noarch perl-if-0.60.800-481.el9.noarch perl-interpreter-5.32.1-481.el9.x86_64 perl-libnet-3.13-4.el9.noarch perl-libs-5.32.1-481.el9.x86_64 perl-mro-1.23-481.el9.x86_64 perl-overload-1.31-481.el9.noarch perl-overloading-0.02-481.el9.noarch perl-parent-0.238-460.el9.noarch perl-podlators-4.14-460.el9.noarch perl-srpm-macros-1-41.el9.noarch perl-subs-1.03-481.el9.noarch perl-vars-1.05-481.el9.noarch pkgconf-1.7.3-10.el9.x86_64 pkgconf-m4-1.7.3-10.el9.noarch pkgconf-pkg-config-1.7.3-10.el9.x86_64 popt-1.18-8.el9.x86_64 publicsuffix-list-dafsa-20210518-3.el9.noarch pyproject-srpm-macros-1.12.0-1.el9.noarch python-srpm-macros-3.9-53.el9.noarch qt5-srpm-macros-5.15.9-1.el9.noarch qt6-srpm-macros-6.6.2-1.el9.noarch readline-8.1-4.el9.x86_64 redhat-release-9.4-0.4.el9.x86_64 redhat-rpm-config-207-1.el9.noarch rpm-4.16.1.3-29.el9.x86_64 rpm-build-4.16.1.3-29.el9.x86_64 rpm-build-libs-4.16.1.3-29.el9.x86_64 rpm-libs-4.16.1.3-29.el9.x86_64 rpmautospec-rpm-macros-0.6.3-1.el9.noarch rust-srpm-macros-17-4.el9.noarch rust-srpm-macros-epel-26.3-1.el9.noarch sed-4.8-9.el9.x86_64 setup-2.13.7-10.el9.noarch shadow-utils-4.9-8.el9.x86_64 sqlite-libs-3.34.1-7.el9_3.x86_64 systemd-libs-252-32.el9_4.x86_64 tar-1.34-6.el9_1.x86_64 tzdata-2024a-1.el9.noarch unzip-6.0-56.el9.x86_64 util-linux-2.37.4-18.el9.x86_64 util-linux-core-2.37.4-18.el9.x86_64 which-2.21-29.el9.x86_64 xz-5.2.5-8.el9_0.x86_64 xz-libs-5.2.5-8.el9_0.x86_64 zip-3.0-35.el9.x86_64 zlib-1.2.11-40.el9.x86_64 zstd-1.5.1-2.el9.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1717372800 Wrote: /builddir/build/SRPMS/samtools-1.20-1.el9.src.rpm Finish: rpmbuild -bs cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/rhel+epel-9-x86_64-1717413963.379560/root/var/log’: No such file or directory INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-9-x86_64-1717413963.379560/root/var/log/dnf.log /var/lib/mock/rhel+epel-9-x86_64-1717413963.379560/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-9-x86_64-1717413963.379560/root/var/log/dnf.rpm.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-5rh5i_yn/samtools/samtools.spec) Config(child) 26 minutes 7 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-1.20-1.el9.src.rpm) Config(rhel+epel-9-x86_64) Start: chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-x86_64-1717413963.379560/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 from host and used with --installroot: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.19.2-1.fc39.noarch python3-dnf-plugins-core-4.6.0-1.fc39.noarch yum-4.19.2-1.fc39.noarch dnf5-5.1.17-1.fc39.x86_64 dnf5-plugins-5.1.17-1.fc39.x86_64 Finish: chroot init Start: build phase for samtools-1.20-1.el9.src.rpm Start: build setup for samtools-1.20-1.el9.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1717372800 Wrote: /builddir/build/SRPMS/samtools-1.20-1.el9.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 46 kB/s | 1.8 kB 00:00 Copr repository 219 kB/s | 21 kB 00:00 Red Hat Enterprise Linux - BaseOS 24 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux - AppStream 26 kB/s | 4.5 kB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 29 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 9 - x86_64 345 kB/s | 12 kB 00:00 Package perl-Getopt-Long-1:2.52-4.el9.noarch is already installed. Package perl-interpreter-4:5.32.1-481.el9.x86_64 is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: gcc x86_64 11.4.1-3.el9 appstream 32 M htslib-devel x86_64 1.20-1.el9 copr_base 104 k htslib-tools x86_64 1.20-1.el9 copr_base 660 k make x86_64 1:4.3-8.el9 baseos 541 k ncurses-devel x86_64 6.2-10.20210508.el9 appstream 732 k perl-FindBin noarch 1.51-481.el9 appstream 14 k perl-lib x86_64 0.65-481.el9 appstream 15 k zlib-devel x86_64 1.2.11-40.el9 appstream 47 k Installing dependencies: annobin x86_64 12.31-2.el9 appstream 1.0 M cpp x86_64 11.4.1-3.el9 appstream 11 M gcc-plugin-annobin x86_64 11.4.1-3.el9 appstream 49 k glibc-devel x86_64 2.34-100.el9_4.2 appstream 42 k glibc-headers x86_64 2.34-100.el9_4.2 appstream 548 k htslib x86_64 1.20-1.el9 copr_base 546 k kernel-headers x86_64 5.14.0-427.18.1.el9_4 appstream 7.4 M libedit x86_64 3.1-38.20210216cvs.el9 baseos 107 k libmpc x86_64 1.2.1-4.el9 appstream 65 k libxcrypt-devel x86_64 4.4.18-3.el9 appstream 32 k llvm-libs x86_64 17.0.6-5.el9 appstream 25 M ncurses-c++-libs x86_64 6.2-10.20210508.el9 appstream 39 k Transaction Summary ================================================================================ Install 20 Packages Total download size: 79 M Installed size: 234 M Downloading Packages: (1/20): htslib-devel-1.20-1.el9.x86_64.rpm 1.4 MB/s | 104 kB 00:00 (2/20): htslib-1.20-1.el9.x86_64.rpm 5.3 MB/s | 546 kB 00:00 (3/20): htslib-tools-1.20-1.el9.x86_64.rpm 5.8 MB/s | 660 kB 00:00 (4/20): libedit-3.1-38.20210216cvs.el9.x86_64.r 507 kB/s | 107 kB 00:00 (5/20): libmpc-1.2.1-4.el9.x86_64.rpm 320 kB/s | 65 kB 00:00 (6/20): libxcrypt-devel-4.4.18-3.el9.x86_64.rpm 352 kB/s | 32 kB 00:00 (7/20): make-4.3-8.el9.x86_64.rpm 1.7 MB/s | 541 kB 00:00 (8/20): ncurses-c++-libs-6.2-10.20210508.el9.x8 400 kB/s | 39 kB 00:00 (9/20): zlib-devel-1.2.11-40.el9.x86_64.rpm 411 kB/s | 47 kB 00:00 (10/20): gcc-plugin-annobin-11.4.1-3.el9.x86_64 627 kB/s | 49 kB 00:00 (11/20): ncurses-devel-6.2-10.20210508.el9.x86_ 2.3 MB/s | 732 kB 00:00 (12/20): annobin-12.31-2.el9.x86_64.rpm 6.1 MB/s | 1.0 MB 00:00 (13/20): perl-FindBin-1.51-481.el9.noarch.rpm 60 kB/s | 14 kB 00:00 (14/20): perl-lib-0.65-481.el9.x86_64.rpm 134 kB/s | 15 kB 00:00 (15/20): llvm-libs-17.0.6-5.el9.x86_64.rpm 31 MB/s | 25 MB 00:00 (16/20): cpp-11.4.1-3.el9.x86_64.rpm 11 MB/s | 11 MB 00:00 (17/20): glibc-devel-2.34-100.el9_4.2.x86_64.rp 297 kB/s | 42 kB 00:00 (18/20): kernel-headers-5.14.0-427.18.1.el9_4.x 32 MB/s | 7.4 MB 00:00 (19/20): gcc-11.4.1-3.el9.x86_64.rpm 34 MB/s | 32 MB 00:00 (20/20): glibc-headers-2.34-100.el9_4.2.x86_64. 3.8 MB/s | 548 kB 00:00 -------------------------------------------------------------------------------- Total 43 MB/s | 79 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-4.el9.x86_64 1/20 Installing : htslib-1.20-1.el9.x86_64 2/20 Installing : cpp-11.4.1-3.el9.x86_64 3/20 Installing : glibc-headers-2.34-100.el9_4.2.x86_64 4/20 Installing : kernel-headers-5.14.0-427.18.1.el9_4.x86_64 5/20 Installing : glibc-devel-2.34-100.el9_4.2.x86_64 6/20 Installing : libxcrypt-devel-4.4.18-3.el9.x86_64 7/20 Installing : ncurses-c++-libs-6.2-10.20210508.el9.x86_64 8/20 Installing : make-1:4.3-8.el9.x86_64 9/20 Installing : gcc-11.4.1-3.el9.x86_64 10/20 Running scriptlet: gcc-11.4.1-3.el9.x86_64 10/20 Installing : libedit-3.1-38.20210216cvs.el9.x86_64 11/20 Installing : llvm-libs-17.0.6-5.el9.x86_64 12/20 Installing : annobin-12.31-2.el9.x86_64 13/20 Running scriptlet: annobin-12.31-2.el9.x86_64 13/20 Installing : gcc-plugin-annobin-11.4.1-3.el9.x86_64 14/20 Running scriptlet: gcc-plugin-annobin-11.4.1-3.el9.x86_64 14/20 Installing : ncurses-devel-6.2-10.20210508.el9.x86_64 15/20 Installing : htslib-devel-1.20-1.el9.x86_64 16/20 Installing : htslib-tools-1.20-1.el9.x86_64 17/20 Installing : perl-lib-0.65-481.el9.x86_64 18/20 Installing : perl-FindBin-1.51-481.el9.noarch 19/20 Installing : zlib-devel-1.2.11-40.el9.x86_64 20/20 Running scriptlet: zlib-devel-1.2.11-40.el9.x86_64 20/20 Verifying : htslib-1.20-1.el9.x86_64 1/20 Verifying : htslib-devel-1.20-1.el9.x86_64 2/20 Verifying : htslib-tools-1.20-1.el9.x86_64 3/20 Verifying : libedit-3.1-38.20210216cvs.el9.x86_64 4/20 Verifying : make-1:4.3-8.el9.x86_64 5/20 Verifying : libmpc-1.2.1-4.el9.x86_64 6/20 Verifying : libxcrypt-devel-4.4.18-3.el9.x86_64 7/20 Verifying : ncurses-devel-6.2-10.20210508.el9.x86_64 8/20 Verifying : ncurses-c++-libs-6.2-10.20210508.el9.x86_64 9/20 Verifying : zlib-devel-1.2.11-40.el9.x86_64 10/20 Verifying : gcc-plugin-annobin-11.4.1-3.el9.x86_64 11/20 Verifying : perl-FindBin-1.51-481.el9.noarch 12/20 Verifying : annobin-12.31-2.el9.x86_64 13/20 Verifying : cpp-11.4.1-3.el9.x86_64 14/20 Verifying : llvm-libs-17.0.6-5.el9.x86_64 15/20 Verifying : perl-lib-0.65-481.el9.x86_64 16/20 Verifying : gcc-11.4.1-3.el9.x86_64 17/20 Verifying : kernel-headers-5.14.0-427.18.1.el9_4.x86_64 18/20 Verifying : glibc-devel-2.34-100.el9_4.2.x86_64 19/20 Verifying : glibc-headers-2.34-100.el9_4.2.x86_64 20/20 Installed products updated. Installed: annobin-12.31-2.el9.x86_64 cpp-11.4.1-3.el9.x86_64 gcc-11.4.1-3.el9.x86_64 gcc-plugin-annobin-11.4.1-3.el9.x86_64 glibc-devel-2.34-100.el9_4.2.x86_64 glibc-headers-2.34-100.el9_4.2.x86_64 htslib-1.20-1.el9.x86_64 htslib-devel-1.20-1.el9.x86_64 htslib-tools-1.20-1.el9.x86_64 kernel-headers-5.14.0-427.18.1.el9_4.x86_64 libedit-3.1-38.20210216cvs.el9.x86_64 libmpc-1.2.1-4.el9.x86_64 libxcrypt-devel-4.4.18-3.el9.x86_64 llvm-libs-17.0.6-5.el9.x86_64 make-1:4.3-8.el9.x86_64 ncurses-c++-libs-6.2-10.20210508.el9.x86_64 ncurses-devel-6.2-10.20210508.el9.x86_64 perl-FindBin-1.51-481.el9.noarch perl-lib-0.65-481.el9.x86_64 zlib-devel-1.2.11-40.el9.x86_64 Complete! Finish: build setup for samtools-1.20-1.el9.src.rpm Start: rpmbuild samtools-1.20-1.el9.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1717372800 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.6NTjU4 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf samtools-1.20 + /usr/bin/bzip2 -dc /builddir/build/SOURCES/samtools-1.20.tar.bz2 + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd samtools-1.20 + /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.h7tyB6 + umask 022 + cd /builddir/build/BUILD + cd samtools-1.20 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' + 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' ./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 + 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-1.20/configure + diff -u ./htslib-1.20/configure.backup ./htslib-1.20/configure + mv ./htslib-1.20/configure.backup ./htslib-1.20/configure + /usr/bin/sed -r --in-place=.backup 's/^char $\*f$ ;/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.20/configure + diff -u ./htslib-1.20/configure.backup ./htslib-1.20/configure + mv ./htslib-1.20/configure.backup ./htslib-1.20/configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 ;/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.20/configure + diff -u ./htslib-1.20/configure.backup ./htslib-1.20/configure + mv ./htslib-1.20/configure.backup ./htslib-1.20/configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.20/configure + diff -u ./htslib-1.20/configure.backup ./htslib-1.20/configure + mv ./htslib-1.20/configure.backup ./htslib-1.20/configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \$.*\$$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \$.*\$$/extern char \\1;/p'\''"#' ./htslib-1.20/configure + diff -u ./htslib-1.20/configure.backup ./htslib-1.20/configure + mv ./htslib-1.20/configure.backup ./htslib-1.20/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-1.20/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./htslib-1.20/config.sub ++ basename ./htslib-1.20/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./htslib-1.20/config.sub '/usr/lib/rpm/redhat/config.sub' -> './htslib-1.20/config.sub' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./htslib-1.20/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./htslib-1.20/config.guess ++ basename ./htslib-1.20/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./htslib-1.20/config.guess '/usr/lib/rpm/redhat/config.guess' -> './htslib-1.20/config.guess' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh + ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --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 --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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' --prefix=/usr --with-htslib=system checking for gawk... gawk checking for x86_64-redhat-linux-gnu-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 -j2 V=1 VERBOSE=1 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o bam_stat.o bam_stat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.20"' > 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 "' >> 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o bam2bcf.o bam2bcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o sample.o sample.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o bam2depth.o bam2depth.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o phase.o phase.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o coverage.o coverage.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o padding.o padding.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o bedcov.o bedcov.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o bamshuf.o bamshuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o dict.o dict.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o stats.o stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o reference.o reference.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o reset.o reset.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o bedidx.o bedidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o bam.o bam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz -lpthread lto-wrapper: warning: using serial compilation of 9 LTRANS jobs + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.RF7dga + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64 ++ dirname /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64 + cd samtools-1.20 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/share/man/man1 /usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin /usr/bin/install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin /usr/bin/install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin /usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/share/man/man1 ++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/zoom2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/blast2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/bowtie2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/export2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/fasta-sanitize.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/interpolate_sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/novo2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/plot-ampliconstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/plot-bamstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/psl2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/sam2vcf.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/samtools.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/seq_cache_populate.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/soap2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/wgsim_eval.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/zoom2sam.pl + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.20-1.el9 --unique-debug-suffix -1.20-1.el9.x86_64 --unique-debug-src-base samtools-1.20-1.el9.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.20 extracting debug info from /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/ace2sam extracting debug info from /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/maq2sam-long extracting debug info from /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/maq2sam-short extracting debug info from /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/md5fa extracting debug info from /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/md5sum-lite extracting debug info from /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/samtools extracting debug info from /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/bin/wgsim original debug info size: 2224kB, size after compression: 1992kB /usr/bin/sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match. 2892 blocks + /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/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.woD2i3 + umask 022 + cd /builddir/build/BUILD + cd samtools-1.20 + ldd samtools + grep -E '/lib(64)?/libhts\.so\.' libhts.so.3 => /lib64/libhts.so.3 (0x00007ff7b8bc3000) + 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-1.20/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.20/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.20/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.20/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.20/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.20/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.20/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.20/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok bgzip -c -b 65272 -s 5 /tmp/Usj4TC0RHZ/bgzip.dat.gz .. ok bgzip -c -b 979200 -s 6 /tmp/Usj4TC0RHZ/bgzip.dat.gz .. ok bgzip -c -b 652804 -s 6 /tmp/Usj4TC0RHZ/bgzip.dat.gz .. ok /builddir/build/BUILD/samtools-1.20/samtools faidx /tmp/Usj4TC0RHZ/faidx.fa 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.20/samtools faidx /tmp/Usj4TC0RHZ/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.20/samtools faidx /tmp/Usj4TC0RHZ/faidx.fa 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.20/samtools faidx /tmp/Usj4TC0RHZ/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.20/samtools faidx /tmp/Usj4TC0RHZ/faidx.fa 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.20/samtools faidx /tmp/Usj4TC0RHZ/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.20/samtools faidx /tmp/Usj4TC0RHZ/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.20/samtools faidx /tmp/Usj4TC0RHZ/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.20/samtools fqidx /tmp/Usj4TC0RHZ/fqidx.fq 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.20/samtools fqidx /tmp/Usj4TC0RHZ/fqidx.fq.gz 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.20/samtools fqidx /tmp/Usj4TC0RHZ/fqidx.fq 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.20/samtools fqidx /tmp/Usj4TC0RHZ/fqidx.fq.gz 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.20/samtools fqidx /tmp/Usj4TC0RHZ/fqidx.fq 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.20/samtools fqidx /tmp/Usj4TC0RHZ/fqidx.fq.gz 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.20/samtools fqidx /tmp/Usj4TC0RHZ/fqidx.fq 1:99998-100007 .. ok .. ok /builddir/build/BUILD/samtools-1.20/samtools fqidx /tmp/Usj4TC0RHZ/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /builddir/build/BUILD/samtools-1.20/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /builddir/build/BUILD/samtools-1.20/test/dat/dict.fa .. ok test_dict: /builddir/build/BUILD/samtools-1.20/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/Usj4TC0RHZ/dict.fa.gz .. ok test_dict: cat /builddir/build/BUILD/samtools-1.20/test/dat/dict.fa | /builddir/build/BUILD/samtools-1.20/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /builddir/build/BUILD/samtools-1.20/samtools dict -AH < /builddir/build/BUILD/samtools-1.20/test/dat/dict.alias.fa .. ok test_dict: /builddir/build/BUILD/samtools-1.20/samtools dict -H -l /builddir/build/BUILD/samtools-1.20/test/dat/dict.alt < /builddir/build/BUILD/samtools-1.20/test/dat/dict.alias.fa .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools view /tmp/Usj4TC0RHZ/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools view /tmp/Usj4TC0RHZ/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools index /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools view -X /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam /tmp/Usj4TC0RHZ/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools view -X /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam /tmp/Usj4TC0RHZ/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools merge -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam.bai /tmp/Usj4TC0RHZ/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools view -X /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam /tmp/Usj4TC0RHZ/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools index /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools index -M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam && cat /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools view -X /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools index -c /builddir/build/BUILD/samtools-1.20/test/dat/auto_indexed.tmp.bam /tmp/Usj4TC0RHZ/auto_indexed.csi && cat /tmp/Usj4TC0RHZ/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools index /builddir/build/BUILD/samtools-1.20/test/dat/auto_indexed.tmp.cram /tmp/Usj4TC0RHZ/auto_indexed.crai && cat /tmp/Usj4TC0RHZ/auto_indexed.crai .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools index -c /builddir/build/BUILD/samtools-1.20/test/dat/auto_indexed.tmp.sam /tmp/Usj4TC0RHZ/auto_indexed.csi && cat /tmp/Usj4TC0RHZ/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools view -@ 2 /tmp/Usj4TC0RHZ/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools view -@ 2 /tmp/Usj4TC0RHZ/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools index -@ 2 /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam /tmp/Usj4TC0RHZ/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam /tmp/Usj4TC0RHZ/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam.bai /tmp/Usj4TC0RHZ/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam /tmp/Usj4TC0RHZ/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools index -@ 2 /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools index -@ 2 -M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam && cat /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.20/test/dat/auto_indexed.tmp.bam /tmp/Usj4TC0RHZ/auto_indexed.csi && cat /tmp/Usj4TC0RHZ/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools index -@ 2 /builddir/build/BUILD/samtools-1.20/test/dat/auto_indexed.tmp.cram /tmp/Usj4TC0RHZ/auto_indexed.crai && cat /tmp/Usj4TC0RHZ/auto_indexed.crai .. ok test_index: /builddir/build/BUILD/samtools-1.20/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.20/test/dat/auto_indexed.tmp.sam /tmp/Usj4TC0RHZ/auto_indexed.csi && cat /tmp/Usj4TC0RHZ/auto_indexed.csi .. ok test_mpileup: /builddir/build/BUILD/samtools-1.20/samtools mpileup -b /tmp/Usj4TC0RHZ/mpileup.bam.list -f /tmp/Usj4TC0RHZ/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.20/samtools mpileup -b /tmp/Usj4TC0RHZ/mpileup.cram.list -f /tmp/Usj4TC0RHZ/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.20/samtools mpileup -b /tmp/Usj4TC0RHZ/mpileup.bam.urllist -f /tmp/Usj4TC0RHZ/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.20/samtools mpileup -b /tmp/Usj4TC0RHZ/mpileup.cram.urllist -f /tmp/Usj4TC0RHZ/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.20/samtools mpileup -B --ff 0x14 -f /tmp/Usj4TC0RHZ/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Usj4TC0RHZ/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.20/samtools mpileup -B --ff 0x14 -f /tmp/Usj4TC0RHZ/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Usj4TC0RHZ/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.20/samtools mpileup /builddir/build/BUILD/samtools-1.20/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/Usj4TC0RHZ/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/Usj4TC0RHZ/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/Usj4TC0RHZ/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/Usj4TC0RHZ/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/Usj4TC0RHZ/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/Usj4TC0RHZ/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/Usj4TC0RHZ/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/Usj4TC0RHZ/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/Usj4TC0RHZ/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/Usj4TC0RHZ/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/Usj4TC0RHZ/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/Usj4TC0RHZ/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/Usj4TC0RHZ/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/Usj4TC0RHZ/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/Usj4TC0RHZ/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/Usj4TC0RHZ/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/Usj4TC0RHZ/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/Usj4TC0RHZ/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/Usj4TC0RHZ/view.001.forn (SAM input) .. ok 68: Count -N /tmp/Usj4TC0RHZ/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/Usj4TC0RHZ/view.001.forn (BAM input) .. ok 70: Count -N /tmp/Usj4TC0RHZ/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/Usj4TC0RHZ/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/Usj4TC0RHZ/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/Usj4TC0RHZ/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/Usj4TC0RHZ/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/Usj4TC0RHZ/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/Usj4TC0RHZ/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/Usj4TC0RHZ/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/Usj4TC0RHZ/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/Usj4TC0RHZ/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/Usj4TC0RHZ/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/Usj4TC0RHZ/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/Usj4TC0RHZ/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/Usj4TC0RHZ/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/Usj4TC0RHZ/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/Usj4TC0RHZ/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/Usj4TC0RHZ/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/Usj4TC0RHZ/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/Usj4TC0RHZ/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/Usj4TC0RHZ/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/Usj4TC0RHZ/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/Usj4TC0RHZ/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/Usj4TC0RHZ/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/Usj4TC0RHZ/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/Usj4TC0RHZ/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/Usj4TC0RHZ/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/Usj4TC0RHZ/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-1.20/samtools view -o /tmp/Usj4TC0RHZ/view.test115.sam -h -d TGCA /tmp/Usj4TC0RHZ/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-1.20/samtools view -c -d TGCA /tmp/Usj4TC0RHZ/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.20/samtools view -o /tmp/Usj4TC0RHZ/view.test117.sam -h -d TGCA /tmp/Usj4TC0RHZ/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-1.20/samtools view -c -d TGCA /tmp/Usj4TC0RHZ/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.20/samtools view -o /tmp/Usj4TC0RHZ/view.test119.sam -h -d TGCA /tmp/Usj4TC0RHZ/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-1.20/samtools view -c -d TGCA /tmp/Usj4TC0RHZ/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/Usj4TC0RHZ/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Usj4TC0RHZ/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.20/samtools view -o /tmp/Usj4TC0RHZ/view.test121.sam -h -D BClong:/tmp/Usj4TC0RHZ/view.001.fobc /tmp/Usj4TC0RHZ/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/Usj4TC0RHZ/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Usj4TC0RHZ/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.20/samtools view -c -D BClong:/tmp/Usj4TC0RHZ/view.001.fobc /tmp/Usj4TC0RHZ/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/Usj4TC0RHZ/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Usj4TC0RHZ/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.20/samtools view -o /tmp/Usj4TC0RHZ/view.test123.sam -h -D BClong:/tmp/Usj4TC0RHZ/view.001.fobc /tmp/Usj4TC0RHZ/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/Usj4TC0RHZ/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Usj4TC0RHZ/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.20/samtools view -c -D BClong:/tmp/Usj4TC0RHZ/view.001.fobc /tmp/Usj4TC0RHZ/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/Usj4TC0RHZ/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Usj4TC0RHZ/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.20/samtools view -o /tmp/Usj4TC0RHZ/view.test125.sam -h -D BClong:/tmp/Usj4TC0RHZ/view.001.fobc /tmp/Usj4TC0RHZ/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/Usj4TC0RHZ/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Usj4TC0RHZ/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.20/samtools view -c -D BClong:/tmp/Usj4TC0RHZ/view.001.fobc /tmp/Usj4TC0RHZ/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-1.20/samtools view -o /tmp/Usj4TC0RHZ/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/Usj4TC0RHZ/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-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/Usj4TC0RHZ/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-1.20/samtools view -o /tmp/Usj4TC0RHZ/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/Usj4TC0RHZ/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-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/Usj4TC0RHZ/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-1.20/samtools view -o /tmp/Usj4TC0RHZ/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/Usj4TC0RHZ/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-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/Usj4TC0RHZ/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-1.20/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.03.bed (BAM input).. ok 351: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.03.bed (BAM input).. ok 352: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.03.bed (CRAM input).. ok 353: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.03.bed (CRAM input).. ok 354: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z (BAM input).. ok 355: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z (BAM input).. ok 356: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z (CRAM input).. ok 357: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z (CRAM input).. ok 358: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z:30 (BAM input).. ok 359: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z:30 (BAM input).. ok 360: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 361: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 362: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 363: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 364: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 365: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 366: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 367: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 368: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 369: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 370: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 371: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 372: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 373: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 374: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed ref2 (BAM input).. ok 375: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed ref2 (BAM input).. ok 376: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed ref2 (CRAM input).. ok 377: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed ref2 (CRAM input).. ok 378: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 379: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 380: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 381: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 382: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 383: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 384: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 385: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 386: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -f 128 (BAM input).. ok 387: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -f 128 (BAM input).. ok 388: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 389: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 390: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -q 5 (BAM input).. ok 391: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -q 5 (BAM input).. ok 392: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 393: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 394: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 395: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 396: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 397: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 398: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 399: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 400: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 401: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 402: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 403: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 404: Region -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 405: Count -L /builddir/build/BUILD/samtools-1.20/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 406: Make BAM with no M5/UR tags .. ok 407: Add @SQ with -t (SAM -> SAM) .. ok 408: Add @SQ with -T (SAM -> SAM) .. ok 409: Add @SQ with -t (BAM -> SAM) .. ok 410: Add @SQ with -T (BAM -> SAM) .. ok 411: Add @SQ with -t (SAM -> BAM) .. ok 412: Add @SQ with -T (SAM -> BAM) .. ok 413: Add @SQ with -t (BAM -> BAM) .. ok 414: Add @SQ with -T (BAM -> BAM) .. ok 415: Add @SQ with -t (SAM -> CRAM) .. ok 416: Add @SQ with -T (SAM -> CRAM) .. ok 417: Add @SQ with -t (BAM -> CRAM) .. ok 418: Add @SQ with -T (BAM -> CRAM) .. ok 419: Make CRAM with no UR field .. ok 420: Decoding CRAM with no UR field via -T .. ok 421: CIGAR B-operator removal .. ok 422: Big SAM -> BAM .. ok 423: Big SAM -> BAM (2 threads) .. ok 424: Big SAM -> BAM (4 threads) .. ok 425: Big SAM -> CRAM .. ok 426: Big SAM -> CRAM (2 threads) .. ok 427: Big SAM -> CRAM (4 threads) .. ok 428: Subsample 0.2 (SAM input) ............ ok 429: Subsample 0.5 (SAM input) ............ ok 430: Subsample 0.8 (SAM input) ............ ok 431: Subsample 0.2 (BAM input) ............ ok 432: Subsample 0.5 (BAM input) ............ ok 433: Subsample 0.8 (BAM input) ............ ok 434: Subsample 0.2 (CRAM input) ............ ok 435: Subsample 0.5 (CRAM input) ............ ok 436: Subsample 0.8 (CRAM input) ............ ok 437: SAM add PG .. ok 438: Unset dup flag, remove dt and do tags .. ok 439: Unmap dup flagged reads. .. ok 440: Unmap dup flagged reads. .. ok 441: fetch pairs .. ok 442: fetch pairs .. ok 443: fetch pairs .. ok test_head: /builddir/build/BUILD/samtools-1.20/samtools head /builddir/build/BUILD/samtools-1.20/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.20/samtools head -h 0 /builddir/build/BUILD/samtools-1.20/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.20/samtools head -h 1 /builddir/build/BUILD/samtools-1.20/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.20/samtools head -h 5 /builddir/build/BUILD/samtools-1.20/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.20/samtools head -h 29 /builddir/build/BUILD/samtools-1.20/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.20/samtools head -h 30 /builddir/build/BUILD/samtools-1.20/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.20/samtools head -n 0 /builddir/build/BUILD/samtools-1.20/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.20/samtools head -n 1 /builddir/build/BUILD/samtools-1.20/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.20/samtools head -n 5 /builddir/build/BUILD/samtools-1.20/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.20/samtools head -h 5 -n 5 < /builddir/build/BUILD/samtools-1.20/test/dat/view.001.sam .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM 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 BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_import: /builddir/build/BUILD/samtools-1.20/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.20/samtools fastq -0 /builddir/build/BUILD/samtools-1.20/test/0.fq .. ok test_import: /builddir/build/BUILD/samtools-1.20/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.20/samtools fastq -0 /builddir/build/BUILD/samtools-1.20/test/0.fq .. ok test_import: /builddir/build/BUILD/samtools-1.20/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /builddir/build/BUILD/samtools-1.20/samtools fastq -s /builddir/build/BUILD/samtools-1.20/test/s.fq .. ok test_import: /builddir/build/BUILD/samtools-1.20/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /builddir/build/BUILD/samtools-1.20/samtools fastq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.20/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /builddir/build/BUILD/samtools-1.20/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.20/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.20/samtools fastq -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.20/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-1.20/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.20/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /builddir/build/BUILD/samtools-1.20/samtools fastq -N -T RG,BC,QT -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.20/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /builddir/build/BUILD/samtools-1.20/samtools fastq -N -T RG,BC,QT,MD,ia -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.20/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-1.20/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-1.20/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-1.20/samtools import --no-PG test/import/2.interleaved.fq -T "" .. ok test_import: /builddir/build/BUILD/samtools-1.20/samtools import --no-PG test/import/3.interleaved.fq -i .. ok test_import: /builddir/build/BUILD/samtools-1.20/samtools import --no-PG test/import/4.aux.fq -T "*" .. ok test_import: /builddir/build/BUILD/samtools-1.20/samtools import --no-PG test/import/4.aux.fq -T "" .. ok test_import: /builddir/build/BUILD/samtools-1.20/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /builddir/build/BUILD/samtools-1.20/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-1.20/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_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-1.20/samtools fastq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.20/test/bc.fq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.20/test/bc.fq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.20/test/bc.fq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.20/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -N -t -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.20/test/i.fq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.20/test/i.fq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.703.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.20/test/o.fq -2 /builddir/build/BUILD/samtools-1.20/test/o.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fasta -N -1 /builddir/build/BUILD/samtools-1.20/test/o.fa -2 /builddir/build/BUILD/samtools-1.20/test/o.fa /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -N -o /builddir/build/BUILD/samtools-1.20/test/o.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -N -s /tmp/Usj4TC0RHZ/bam2fq.discard.s.fq -0 /tmp/Usj4TC0RHZ/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.013.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.20/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.20/test/i2.fq -0 /builddir/build/BUILD/samtools-1.20/test/0.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.014.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -N -T '' /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -N -t -T '*' /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -N -T '*' -d MD:10 /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -N -T '*' -d NM:0 /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -N -T '*' -d ia /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -d NM:13 -d NM:14 /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -D NM:test/dat/bam2fq.NM-D /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -D MD:test/dat/bam2fq.MD-D /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.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-1.20/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.20/test/bc.fq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.20/test/bc.fq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.20/test/bc.fq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.20/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -N -t -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.20/test/i.fq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.20/test/i.fq -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.20/test/s.fq -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.20/test/1.fq -2 /builddir/build/BUILD/samtools-1.20/test/2.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.703.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -N -1 /builddir/build/BUILD/samtools-1.20/test/o.fq -2 /builddir/build/BUILD/samtools-1.20/test/o.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fasta -@ 2 -N -1 /builddir/build/BUILD/samtools-1.20/test/o.fa -2 /builddir/build/BUILD/samtools-1.20/test/o.fa /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -N -o /builddir/build/BUILD/samtools-1.20/test/o.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -N -s /tmp/Usj4TC0RHZ/bam2fq.discard.s.fq -0 /tmp/Usj4TC0RHZ/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.013.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.20/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.20/test/i2.fq -0 /builddir/build/BUILD/samtools-1.20/test/0.fq /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.014.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -N -T '' /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -N -t -T '*' /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -N -T '*' -d MD:10 /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -N -T '*' -d NM:0 /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -N -T '*' -d ia /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -d NM:13 -d NM:14 /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.20/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /builddir/build/BUILD/samtools-1.20/test/dat/bam2fq.001.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-1.20/samtools stats -r /builddir/build/BUILD/samtools-1.20/test/stat/test.fa /builddir/build/BUILD/samtools-1.20/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -r /builddir/build/BUILD/samtools-1.20/test/stat/test.fa /builddir/build/BUILD/samtools-1.20/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -r /builddir/build/BUILD/samtools-1.20/test/stat/test.fa /builddir/build/BUILD/samtools-1.20/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -r /builddir/build/BUILD/samtools-1.20/test/stat/test.fa /builddir/build/BUILD/samtools-1.20/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -r /builddir/build/BUILD/samtools-1.20/test/stat/test.fa /builddir/build/BUILD/samtools-1.20/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -r /builddir/build/BUILD/samtools-1.20/test/stat/test.fa -i 0 /builddir/build/BUILD/samtools-1.20/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -r /builddir/build/BUILD/samtools-1.20/test/stat/test.fa /builddir/build/BUILD/samtools-1.20/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -r /builddir/build/BUILD/samtools-1.20/test/stat/test.fa /builddir/build/BUILD/samtools-1.20/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.20/test/stat/test.fa /builddir/build/BUILD/samtools-1.20/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.20/test/stat/test.fa /builddir/build/BUILD/samtools-1.20/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -t /builddir/build/BUILD/samtools-1.20/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.20/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -g 4 -t /builddir/build/BUILD/samtools-1.20/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.20/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -g 4 /builddir/build/BUILD/samtools-1.20/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.20/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.20/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.20/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.20/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /builddir/build/BUILD/samtools-1.20/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /builddir/build/BUILD/samtools-1.20/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats /builddir/build/BUILD/samtools-1.20/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /builddir/build/BUILD/samtools-1.20/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -I s1 /builddir/build/BUILD/samtools-1.20/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -I grp2 /builddir/build/BUILD/samtools-1.20/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -I grp3 /builddir/build/BUILD/samtools-1.20/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -I Sample /builddir/build/BUILD/samtools-1.20/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.20/samtools stats -r /builddir/build/BUILD/samtools-1.20/test/mpileup/ce.fa /builddir/build/BUILD/samtools-1.20/test/stat/15.big_del.sam | tail -n+4 .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -s 1 -O sam -b /tmp/UmiV08tXch - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/Usj4TC0RHZ/merge.tag.1.bam /tmp/Usj4TC0RHZ/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/Usj4TC0RHZ/merge.tag.3.bam /tmp/Usj4TC0RHZ/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge --no-PG -O SAM - /builddir/build/BUILD/samtools-1.20/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.20/test/merge/merge.bed - /tmp/Usj4TC0RHZ/merge.bed.1.bam /tmp/Usj4TC0RHZ/merge.bed.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge --no-PG -r -O SAM - /builddir/build/BUILD/samtools-1.20/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 -s 1 -O sam -b /tmp/wcY7QmuGsR - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/Usj4TC0RHZ/merge.tag.1.bam /tmp/Usj4TC0RHZ/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/Usj4TC0RHZ/merge.tag.3.bam /tmp/Usj4TC0RHZ/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 --no-PG -O SAM - /builddir/build/BUILD/samtools-1.20/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.20/test/merge/merge.bed - /tmp/Usj4TC0RHZ/merge.bed.1.bam /tmp/Usj4TC0RHZ/merge.bed.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.20/samtools merge -@ 2 --no-PG -r -O SAM - /builddir/build/BUILD/samtools-1.20/test/merge/test_no_pg_rg_co.sam .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /tmp/Usj4TC0RHZ/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -f /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /tmp/Usj4TC0RHZ/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -o /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /tmp/Usj4TC0RHZ/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -N -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -t RG -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -n -t RG -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -t AS -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -t FI -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort --template-coordinate -m 10M /builddir/build/BUILD/samtools-1.20/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools reset /builddir/build/BUILD/samtools-1.20/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.20/samtools sort -M -K10 -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools reset /builddir/build/BUILD/samtools-1.20/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.20/samtools sort -M -K10 -I /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools reset /builddir/build/BUILD/samtools-1.20/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.20/samtools sort -MH -K10 -I /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /tmp/Usj4TC0RHZ/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /tmp/Usj4TC0RHZ/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam /tmp/Usj4TC0RHZ/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -N -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -t RG -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -n -t RG -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -t AS -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -t FI -m 10M /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 --template-coordinate -m 10M /builddir/build/BUILD/samtools-1.20/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools reset /builddir/build/BUILD/samtools-1.20/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -M -K10 -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools reset /builddir/build/BUILD/samtools-1.20/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -M -K10 -I /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.20/samtools reset /builddir/build/BUILD/samtools-1.20/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.20/samtools sort -@ 2 -MH -K10 -I /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_collate: /builddir/build/BUILD/samtools-1.20/samtools collate --output-fmt=sam -O /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.20/samtools collate -o /builddir/build/BUILD/samtools-1.20/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.20/samtools collate -o /builddir/build/BUILD/samtools-1.20/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.20/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.20/samtools collate --output-fmt=sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.20/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.20/samtools collate --output-fmt=sam -f /builddir/build/BUILD/samtools-1.20/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.20/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.20/samtools collate --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.20/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.20/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.20/samtools collate -@ 2 --output-fmt=sam -O /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.20/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.20/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.20/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.20/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.20/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.20/samtools collate -@ 2 --output-fmt=sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.20/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.20/samtools collate -@ 2 --output-fmt=sam -f /builddir/build/BUILD/samtools-1.20/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.20/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.20/samtools collate -@ 2 --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.20/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.20/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.20/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-1.20/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.20/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.20/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/sanitize.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_draft.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_bounds.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.20/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-1.20/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.20/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.20/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/sanitize.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_draft.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.20/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.20/test/fixmate/mod_bounds.sam - .. ok /builddir/build/BUILD/samtools-1.20/samtools calmd -uAr /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.ref.fa .. ok /builddir/build/BUILD/samtools-1.20/samtools calmd -@ 2 -uAr /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.ref.fa .. ok test_idxstat: /builddir/build/BUILD/samtools-1.20/samtools idxstats /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam .. ok test_idxstat: /builddir/build/BUILD/samtools-1.20/samtools idxstats /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.cram .. ok test_idxstat: /builddir/build/BUILD/samtools-1.20/samtools idxstats /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.sam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.20/samtools quickcheck /builddir/build/BUILD/samtools-1.20/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.20/samtools quickcheck /builddir/build/BUILD/samtools-1.20/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.20/samtools quickcheck /builddir/build/BUILD/samtools-1.20/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.20/samtools quickcheck /builddir/build/BUILD/samtools-1.20/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.20/samtools quickcheck /builddir/build/BUILD/samtools-1.20/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.20/samtools quickcheck /builddir/build/BUILD/samtools-1.20/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.20/samtools quickcheck /builddir/build/BUILD/samtools-1.20/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.20/samtools quickcheck /builddir/build/BUILD/samtools-1.20/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.20/samtools quickcheck /builddir/build/BUILD/samtools-1.20/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.20/samtools quickcheck /builddir/build/BUILD/samtools-1.20/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.20/samtools quickcheck -v /builddir/build/BUILD/samtools-1.20/test/quickcheck/1.quickcheck.badeof.bam /builddir/build/BUILD/samtools-1.20/test/quickcheck/2.quickcheck.badheader.bam /builddir/build/BUILD/samtools-1.20/test/quickcheck/3.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.20/test/quickcheck/4.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.20/test/quickcheck/5.quickcheck.scramble30.truncated.cram /builddir/build/BUILD/samtools-1.20/test/quickcheck/6.quickcheck.cram21.ok.cram /builddir/build/BUILD/samtools-1.20/test/quickcheck/7.quickcheck.cram30.ok.cram /builddir/build/BUILD/samtools-1.20/test/quickcheck/8.quickcheck.cram21.truncated.cram /builddir/build/BUILD/samtools-1.20/test/quickcheck/9.quickcheck.cram30.truncated.cram /builddir/build/BUILD/samtools-1.20/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.20/samtools quickcheck -uv /builddir/build/BUILD/samtools-1.20/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /builddir/build/BUILD/samtools-1.20/samtools reheader /builddir/build/BUILD/samtools-1.20/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.20/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.20/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.20/samtools reheader /builddir/build/BUILD/samtools-1.20/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.20/test/dat/view.001.tmp.v21.cram | /builddir/build/BUILD/samtools-1.20/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.20/samtools reheader /builddir/build/BUILD/samtools-1.20/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.20/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.20/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.20/samtools reheader --in-place /builddir/build/BUILD/samtools-1.20/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.20/test/dat/view.001.tmp.v21.cram && /builddir/build/BUILD/samtools-1.20/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.20/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.20/samtools reheader --in-place /builddir/build/BUILD/samtools-1.20/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.20/test/dat/view.001.tmp.v30.cram && /builddir/build/BUILD/samtools-1.20/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.20/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.20/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.20/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.20/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.20/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.20/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.20/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -O sam -m orphan_only /builddir/build/BUILD/samtools-1.20/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -O sam -R '1#9' /builddir/build/BUILD/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.20/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.20/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -@ 2 -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -@ 2 -O sam -m orphan_only /builddir/build/BUILD/samtools-1.20/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -@ 2 -O sam -R '1#9' /builddir/build/BUILD/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.20/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.20/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.20/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.20/test/addrprg/1_fixup.sam .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.20/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-1.20/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.20/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-1.20/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.20/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-1.20/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -O sam -r --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -S -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/8_optical_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.20/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.20/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/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-1.20/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/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-1.20/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/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-1.20/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/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-1.20/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/17_read_group.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /builddir/build/BUILD/samtools-1.20/test/markdup/18_primary_duplicate_count.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.20/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-1.20/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.20/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-1.20/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.20/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-1.20/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 -O sam -r --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 -S -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/8_optical_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.20/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.20/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/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-1.20/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/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-1.20/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/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-1.20/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/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-1.20/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /builddir/build/BUILD/samtools-1.20/test/markdup/17_read_group.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.20/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /builddir/build/BUILD/samtools-1.20/test/markdup/18_primary_duplicate_count.sam - .. ok test_bedcov: /builddir/build/BUILD/samtools-1.20/samtools bedcov /builddir/build/BUILD/samtools-1.20/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.20/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.20/samtools bedcov -j /builddir/build/BUILD/samtools-1.20/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.20/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.20/samtools bedcov -g512 -G2048 /builddir/build/BUILD/samtools-1.20/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.20/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.20/samtools bedcov -c /builddir/build/BUILD/samtools-1.20/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.20/test/bedcov/bedcov.bam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.20/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.unk.sam -p 5 -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.20/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.20/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split --output-fmt sam -d RG -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.20/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split --output-fmt sam -d an -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.20/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split --output-fmt sam -d an -M 3 -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.20/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split --output-fmt sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.d_nn.%!.%. -d nn -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.d_nn.unk.sam /builddir/build/BUILD/samtools-1.20/test/split/split_d_nn.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split --output-fmt sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.d_nn.0unk.sam /builddir/build/BUILD/samtools-1.20/test/split/split_d_nn.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.20/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.unk.sam -p 5 -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.20/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.20/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split -@ 2 --output-fmt sam -d RG -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.20/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split -@ 2 --output-fmt sam -d an -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.20/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.20/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.d_nn.%!.%. -d nn -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.d_nn.unk.sam /builddir/build/BUILD/samtools-1.20/test/split/split_d_nn.sam .. ok test_split: /builddir/build/BUILD/samtools-1.20/samtools split -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.20/test/split/split.tmp.d_nn.0unk.sam /builddir/build/BUILD/samtools-1.20/test/split/split_d_nn.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.20/samtools view -h --no-PG /tmp/Usj4TC0RHZ/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.20/samtools view -h --no-PG /tmp/Usj4TC0RHZ/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /builddir/build/BUILD/samtools-1.20/samtools view -h --no-PG -L /builddir/build/BUILD/samtools-1.20/test/large_pos/test.bed /tmp/Usj4TC0RHZ/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.20/samtools sort -O sam --no-PG -m 10M /builddir/build/BUILD/samtools-1.20/test/large_pos/longref_name.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.20/samtools merge -O sam --no-PG - /builddir/build/BUILD/samtools-1.20/test/large_pos/longref.sam /builddir/build/BUILD/samtools-1.20/test/large_pos/longref2.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.20/samtools depth /builddir/build/BUILD/samtools-1.20/test/large_pos/longref.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.20/samtools depth -b /builddir/build/BUILD/samtools-1.20/test/large_pos/test.bed /builddir/build/BUILD/samtools-1.20/test/large_pos/longref.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.20/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/Usj4TC0RHZ/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.20/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /builddir/build/BUILD/samtools-1.20/samtools fixmate -O sam --no-PG - - | /builddir/build/BUILD/samtools-1.20/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test2.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.20/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test2.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.20/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_hard_clipped.expected.sam /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_soft_clipped.expected.sam /builddir/build/BUILD/samtools-1.20/test/ampliconclip/1_soft_clipped_strand.expected.sam /builddir/build/BUILD/samtools-1.20/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.20/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.20/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.20/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.20/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.20/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.20/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.20/samtools reset | /builddir/build/BUILD/samtools-1.20/samtools view .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset < /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.20/samtools view .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.20/samtools view .. ok test_reset: cat /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.20/samtools reset -o /builddir/build/BUILD/samtools-1.20/test/reset/output.tmp.sam .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset -o /builddir/build/BUILD/samtools-1.20/test/reset/output.tmp.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.bam .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset -o /builddir/build/BUILD/samtools-1.20/test/reset/output.tmp.sam /builddir/build/BUILD/samtools-1.20/test/dat/test_input_1_a.cram .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset --reject-PG bwa_index /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.20/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.20/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset --reject-PG sam_to_fixed_bam /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.20/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.20/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset --reject-PG bwa_index --no-PG /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.20/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.20/test/reset/output.tmp.sam -e"@PG" .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset --reject-PG bwa /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam --no-RG -o /builddir/build/BUILD/samtools-1.20/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset --reject-PG bwa /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /builddir/build/BUILD/samtools-1.20/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset --reject-PG bwa /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /builddir/build/BUILD/samtools-1.20/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset --reject-PG bwa /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /builddir/build/BUILD/samtools-1.20/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset --reject-PG bwa /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /builddir/build/BUILD/samtools-1.20/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset --reject-PG bwa /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /builddir/build/BUILD/samtools-1.20/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset --reject-PG bwa /builddir/build/BUILD/samtools-1.20/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /builddir/build/BUILD/samtools-1.20/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.20/samtools reset /builddir/build/BUILD/samtools-1.20/test/reset/seq.sam -o /builddir/build/BUILD/samtools-1.20/test/reset/output .. ok Number of tests: total .. 934 passed .. 903 failed .. 0 expected failure .. 31 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: 53 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: 65 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-1.20-1.el9.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.66yI6u + umask 022 + cd /builddir/build/BUILD + cd samtools-1.20 + DOCDIR=/builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/share/doc/samtools + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/share/doc/samtools + cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/share/doc/samtools + cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/share/doc/samtools + cp -pr NEWS.md /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/share/doc/samtools + cp -pr examples/ /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/share/doc/samtools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.UKyDuY + umask 022 + cd /builddir/build/BUILD + cd samtools-1.20 + LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/share/licenses/samtools + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/share/licenses/samtools + cp -pr LICENSE /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64/usr/share/licenses/samtools + RPM_EC=0 ++ jobs -p + exit 0 Provides: samtools = 1.20-1.el9 samtools(x86-64) = 1.20-1.el9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) 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_1.2.1)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) libhts.so.3(HTSLIB_1.9)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: samtools-debugsource-1.20-1.el9.x86_64 Provides: samtools-debugsource = 1.20-1.el9 samtools-debugsource(x86-64) = 1.20-1.el9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: samtools-debuginfo-1.20-1.el9.x86_64 Provides: debuginfo(build-id) = 1a2cf6e77a8f06d6857ac8a2be766cc49cac9128 debuginfo(build-id) = 23313eebfb6894331c3ee0adc9d0cadcb1368f2b debuginfo(build-id) = 7c3fccdae62f057bd917d6336a419ac7ec760884 debuginfo(build-id) = 801f860d60219f2454cdd0e4384820cc05e325e2 debuginfo(build-id) = 9b5fb9974fb4395a3f6c9ac7ada666f7476e6343 debuginfo(build-id) = bd788c98d96ad74b3ebaa3958128fb7691cc28a2 debuginfo(build-id) = d67bd0535e034676a09381f3179ada173a14f232 samtools-debuginfo = 1.20-1.el9 samtools-debuginfo(x86-64) = 1.20-1.el9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: samtools-debugsource(x86-64) = 1.20-1.el9 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64 Wrote: /builddir/build/RPMS/samtools-debuginfo-1.20-1.el9.x86_64.rpm Wrote: /builddir/build/RPMS/samtools-debugsource-1.20-1.el9.x86_64.rpm Wrote: /builddir/build/RPMS/samtools-1.20-1.el9.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.vpDrRY + umask 022 + cd /builddir/build/BUILD + cd samtools-1.20 + /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.20-1.el9.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild samtools-1.20-1.el9.src.rpm Finish: build phase for samtools-1.20-1.el9.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-9-x86_64-1717413963.379560/root/var/log/dnf.log /var/lib/mock/rhel+epel-9-x86_64-1717413963.379560/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-9-x86_64-1717413963.379560/root/var/log/dnf.rpm.log INFO: Done(/var/lib/copr-rpmbuild/results/samtools-1.20-1.el9.src.rpm) Config(child) 1 minutes 21 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-debuginfo", "epoch": null, "version": "1.20", "release": "1.el9", "arch": "x86_64" }, { "name": "samtools", "epoch": null, "version": "1.20", "release": "1.el9", "arch": "src" }, { "name": "samtools", "epoch": null, "version": "1.20", "release": "1.el9", "arch": "x86_64" }, { "name": "samtools-debugsource", "epoch": null, "version": "1.20", "release": "1.el9", "arch": "x86_64" } ] } RPMResults finished