Warning: Permanently added '13.221.177.235' (ED25519) to the list of known hosts.

You can reproduce this build on your computer by running:

  sudo dnf install copr-rpmbuild
  /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/10066888-epel-9-x86_64 --chroot epel-9-x86_64


Version: 1.6
PID: 62105
Logging PID: 62107
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'build_id': 10066888,
 'buildroot_pkgs': [],
 'chroot': 'epel-9-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '624052c1792453848c83aeb6f9b9daebd1bdd335',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ron/staging/samtools',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'samtools',
 'package_version': '1.23-1',
 'project_dirname': 'staging',
 'project_name': 'staging',
 'project_owner': 'ron',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ron/staging/epel-9-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'ron/staging--ron',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'storage': 0,
 'submitter': 'ron',
 'tags': [],
 'task_id': '10066888-epel-9-x86_64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ron/staging/samtools /var/lib/copr-rpmbuild/workspace/workdir-i8epto6n/samtools --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ron/staging/samtools', '/var/lib/copr-rpmbuild/workspace/workdir-i8epto6n/samtools', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-i8epto6n/samtools'...

Running: git checkout 624052c1792453848c83aeb6f9b9daebd1bdd335 --

cmd: ['git', 'checkout', '624052c1792453848c83aeb6f9b9daebd1bdd335', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-i8epto6n/samtools
rc: 0
stdout: 
stderr: Note: switching to '624052c1792453848c83aeb6f9b9daebd1bdd335'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 624052c automatic import of samtools

Running: dist-git-client sources

cmd: ['dist-git-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-i8epto6n/samtools
rc: 0
stdout: 
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading samtools-1.23.tar.bz2
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o samtools-1.23.tar.bz2 --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/ron/staging/samtools/samtools-1.23.tar.bz2/md5/7ce93103e5a3796c0009f879853837bb/samtools-1.23.tar.bz2
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 9138k  100 9138k    0     0   329M      0 --:--:-- --:--:-- --:--:--  330M
INFO: Reading stdout from command: md5sum samtools-1.23.tar.bz2

tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-i8epto6n/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-i8epto6n/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769509256.406503 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 6.6 starting (python version = 3.14.2, NVR = mock-6.6-1.fc43), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-i8epto6n/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-i8epto6n/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769509256.406503 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-i8epto6n/samtools/samtools.spec)  Config(rhel+epel-9-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 6.6
INFO: Mock Version: 6.6
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-x86_64-bootstrap-1769509256.406503/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using container image: registry.access.redhat.com/ubi9/ubi
INFO: Pulling image: registry.access.redhat.com/ubi9/ubi
INFO: Tagging container image as mock-bootstrap-cde74641-0d60-45fb-8f4f-5d98410a1fab
INFO: Checking that e89dd380e2cf454886aea13596b4c6ab3e21e5b238ef9773db86b828d0215804 image matches host's architecture
INFO: Copy content of container e89dd380e2cf454886aea13596b4c6ab3e21e5b238ef9773db86b828d0215804 to /var/lib/mock/rhel+epel-9-x86_64-bootstrap-1769509256.406503/root
INFO: mounting e89dd380e2cf454886aea13596b4c6ab3e21e5b238ef9773db86b828d0215804 with podman image mount
INFO: image e89dd380e2cf454886aea13596b4c6ab3e21e5b238ef9773db86b828d0215804 as /var/lib/containers/storage/overlay/eb562d236c3b2272d37367e2f489a1366c491ea0d3b0cdfa991daeb91090d450/merged
INFO: umounting image e89dd380e2cf454886aea13596b4c6ab3e21e5b238ef9773db86b828d0215804 (/var/lib/containers/storage/overlay/eb562d236c3b2272d37367e2f489a1366c491ea0d3b0cdfa991daeb91090d450/merged) with podman image umount
INFO: Removing image mock-bootstrap-cde74641-0d60-45fb-8f4f-5d98410a1fab
INFO: Package manager dnf4 detected and used (fallback)
INFO: Not updating bootstrap chroot, bootstrap_image_ready=True
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-x86_64-1769509256.406503/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf4 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.16.1.3-39.el9.x86_64
  python3-dnf-4.14.0-31.el9.noarch
  python3-dnf-plugins-core-4.3.0-24.el9_7.noarch
  yum-4.14.0-31.el9.noarch
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                                  41 kB/s | 1.5 kB     00:00    
Copr repository                                 340 kB/s |  13 kB     00:00    
Red Hat Enterprise Linux - BaseOS                21 kB/s | 4.1 kB     00:00    
Red Hat Enterprise Linux - AppStream             40 kB/s | 4.5 kB     00:00    
Red Hat Enterprise Linux - CodeReady Linux Buil  52 kB/s | 4.5 kB     00:00    
Extra Packages for Enterprise Linux 9 - x86_64   92 kB/s |  23 kB     00:00    
Dependencies resolved.
================================================================================
 Package                     Arch   Version                     Repo       Size
================================================================================
Installing:
 bash                        x86_64 5.1.8-9.el9                 baseos    1.7 M
 bzip2                       x86_64 1.0.8-10.el9_5              baseos     60 k
 coreutils                   x86_64 8.32-39.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 9-17.el9                    epel       15 k
 findutils                   x86_64 1:4.8.0-7.el9               baseos    550 k
 gawk                        x86_64 5.1.0-6.el9                 baseos    1.0 M
 glibc-minimal-langpack      x86_64 2.34-231.el9_7.2            baseos     22 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 9.7-0.7.el9                 baseos     53 k
 redhat-rpm-config           noarch 210-1.el9                   appstream  70 k
 rpm-build                   x86_64 4.16.1.3-39.el9             appstream  66 k
 sed                         x86_64 4.8-9.el9                   baseos    309 k
 tar                         x86_64 2:1.34-9.el9_7              baseos    885 k
 unzip                       x86_64 6.0-59.el9                  baseos    182 k
 util-linux                  x86_64 2.37.4-21.el9               baseos    2.3 M
 which                       x86_64 2.21-30.el9_6               baseos     41 k
 xz                          x86_64 5.2.5-8.el9_0               baseos    230 k
Installing dependencies:
 alternatives                x86_64 1.24-2.el9                  baseos     42 k
 ansible-srpm-macros         noarch 1-16.el9                    epel       21 k
 audit-libs                  x86_64 3.1.5-7.el9                 baseos    119 k
 basesystem                  noarch 11-13.el9                   baseos    8.0 k
 binutils                    x86_64 2.35.2-67.el9_7.1           baseos    4.6 M
 binutils-gold               x86_64 2.35.2-67.el9_7.1           baseos    734 k
 bzip2-libs                  x86_64 1.0.8-10.el9_5              baseos     42 k
 ca-certificates             noarch 2025.2.80_v9.0.305-91.el9   baseos    1.0 M
 coreutils-common            x86_64 8.32-39.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 20250905-1.git377cc42.el9_7 baseos     90 k
 curl                        x86_64 7.76.1-34.el9               baseos    292 k
 cyrus-sasl-lib              x86_64 2.1.27-22.el9               baseos    768 k
 debugedit                   x86_64 5.0-11.el9                  appstream  77 k
 dwz                         x86_64 0.16-1.el9                  appstream 134 k
 ed                          x86_64 1.14.2-12.el9               baseos     78 k
 efi-srpm-macros             noarch 6-4.el9                     appstream  21 k
 elfutils                    x86_64 0.193-1.el9                 baseos    598 k
 elfutils-debuginfod-client  x86_64 0.193-1.el9                 baseos     44 k
 elfutils-default-yama-scope noarch 0.193-1.el9                 baseos    9.7 k
 elfutils-libelf             x86_64 0.193-1.el9                 baseos    205 k
 elfutils-libs               x86_64 0.193-1.el9                 baseos    268 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 3.16-5.el9                  baseos    4.8 M
 fonts-srpm-macros           noarch 1:2.0.5-7.el9.1             appstream  29 k
 forge-srpm-macros           noarch 0.4.0-1.el9                 epel       19 k
 fpc-srpm-macros             noarch 1.3-7.el9                   epel      7.5 k
 gdb-minimal                 x86_64 16.3-2.el9                  appstream 4.4 M
 gdbm-libs                   x86_64 1:1.23-1.el9                baseos     59 k
 ghc-srpm-macros             noarch 1.5.0-6.el9                 appstream 9.0 k
 ghc-srpm-macros-epel        noarch 1.9.1-1.el9                 epel      7.5 k
 glibc                       x86_64 2.34-231.el9_7.2            baseos    2.0 M
 glibc-common                x86_64 2.34-231.el9_7.2            baseos    306 k
 glibc-gconv-extra           x86_64 2.34-231.el9_7.2            baseos    1.7 M
 gmp                         x86_64 1:6.2.0-13.el9              baseos    319 k
 go-srpm-macros              noarch 3.6.0-12.el9_7              appstream  27 k
 go-srpm-macros-epel         noarch 3.8.0-1.el9                 epel       26 k
 groff-base                  x86_64 1.22.4-10.el9               baseos    1.1 M
 json-c                      x86_64 0.14-11.el9                 baseos     45 k
 kernel-srpm-macros          noarch 1.0-14.el9                  appstream  14 k
 keyutils-libs               x86_64 1.6.3-1.el9                 baseos     34 k
 krb5-libs                   x86_64 1.21.1-8.el9_6              baseos    766 k
 libacl                      x86_64 2.3.1-4.el9                 baseos     24 k
 libarchive                  x86_64 3.5.3-6.el9_6               baseos    387 k
 libattr                     x86_64 2.5.1-3.el9                 baseos     20 k
 libblkid                    x86_64 2.37.4-21.el9               baseos    109 k
 libbrotli                   x86_64 1.0.9-7.el9_5               baseos    316 k
 libcap                      x86_64 2.48-10.el9                 baseos     70 k
 libcap-ng                   x86_64 0.8.2-7.el9                 baseos     36 k
 libcom_err                  x86_64 1.46.5-8.el9                baseos     26 k
 libcurl                     x86_64 7.76.1-34.el9               baseos    283 k
 libdb                       x86_64 5.3.28-57.el9_6             baseos    737 k
 libeconf                    x86_64 0.4.1-4.el9                 baseos     30 k
 libevent                    x86_64 2.1.12-8.el9_4              baseos    266 k
 libfdisk                    x86_64 2.37.4-21.el9               baseos    156 k
 libffi                      x86_64 3.4.2-8.el9                 baseos     40 k
 libgcc                      x86_64 11.5.0-11.el9               baseos     85 k
 libgcrypt                   x86_64 1.10.0-11.el9               baseos    510 k
 libgomp                     x86_64 11.5.0-11.el9               baseos    257 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 2.37.4-21.el9               baseos    136 k
 libnghttp2                  x86_64 1.43.0-6.el9                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 3.6-3.el9                   baseos     88 k
 libsemanage                 x86_64 3.6-5.el9_6                 baseos    121 k
 libsepol                    x86_64 3.6-3.el9                   baseos    331 k
 libsigsegv                  x86_64 2.13-4.el9                  baseos     30 k
 libsmartcols                x86_64 2.37.4-21.el9               baseos     65 k
 libssh                      x86_64 0.10.4-17.el9_7             baseos    214 k
 libssh-config               noarch 0.10.4-17.el9_7             baseos    8.1 k
 libstdc++                   x86_64 11.5.0-11.el9               baseos    742 k
 libtasn1                    x86_64 4.16.0-9.el9                baseos     77 k
 libtool-ltdl                x86_64 2.4.6-46.el9                baseos     37 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 2.37.4-21.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 2.9.13-14.el9_7             baseos    747 k
 libzstd                     x86_64 1.5.5-1.el9                 baseos    297 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 6.2-12.20210508.el9         baseos    406 k
 ncurses-base                noarch 6.2-12.20210508.el9         baseos     96 k
 ncurses-libs                x86_64 6.2-12.20210508.el9         baseos    328 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 2.6.8-4.el9                 baseos    290 k
 openssl                     x86_64 1:3.5.1-5.el9_7             baseos    1.5 M
 openssl-fips-provider       x86_64 3.0.7-8.el9                 baseos    9.2 k
 openssl-fips-provider-so    x86_64 3.0.7-8.el9                 baseos    576 k
 openssl-libs                x86_64 1:3.5.1-5.el9_7             baseos    2.3 M
 p11-kit                     x86_64 0.25.3-3.el9_5              baseos    536 k
 p11-kit-trust               x86_64 0.25.3-3.el9_5              baseos    144 k
 pam                         x86_64 1.5.1-26.el9_6              baseos    622 k
 pcre                        x86_64 8.44-4.el9                  baseos    200 k
 pcre2                       x86_64 10.40-6.el9                 baseos    236 k
 pcre2-syntax                noarch 10.40-6.el9                 baseos    144 k
 perl-AutoLoader             noarch 5.74-481.1.el9_6            appstream  21 k
 perl-B                      x86_64 1.80-481.1.el9_6            appstream 180 k
 perl-Carp                   noarch 1.50-460.el9                appstream  31 k
 perl-Class-Struct           noarch 0.66-481.1.el9_6            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 1.30-481.1.el9_6            appstream  15 k
 perl-Exporter               noarch 5.74-461.el9                appstream  34 k
 perl-Fcntl                  x86_64 1.13-481.1.el9_6            appstream  20 k
 perl-File-Basename          noarch 2.85-481.1.el9_6            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 1.09-481.1.el9_6            appstream  17 k
 perl-FileHandle             noarch 2.03-481.1.el9_6            appstream  15 k
 perl-Getopt-Long            noarch 1:2.52-4.el9                appstream  64 k
 perl-Getopt-Std             noarch 1.12-481.1.el9_6            appstream  15 k
 perl-HTTP-Tiny              noarch 0.076-462.el9               appstream  57 k
 perl-IO                     x86_64 1.43-481.1.el9_6            appstream  88 k
 perl-IO-Socket-IP           noarch 0.41-5.el9                  appstream  45 k
 perl-IO-Socket-SSL          noarch 2.073-2.el9                 appstream 221 k
 perl-IPC-Open3              noarch 1.21-481.1.el9_6            appstream  22 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 1.94-3.el9                  appstream 414 k
 perl-POSIX                  x86_64 1.94-481.1.el9_6            appstream  96 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 4:1.56-462.el9              appstream  75 k
 perl-SelectSaver            noarch 1.02-481.1.el9_6            appstream  11 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 1.08-481.1.el9_6            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 2.27-481.1.el9_6            appstream  16 k
 perl-constant               noarch 1.33-461.el9                appstream  25 k
 perl-if                     noarch 0.60.800-481.1.el9_6        appstream  14 k
 perl-interpreter            x86_64 4:5.32.1-481.1.el9_6        appstream  70 k
 perl-libnet                 noarch 3.13-4.el9                  appstream 134 k
 perl-libs                   x86_64 4:5.32.1-481.1.el9_6        appstream 2.2 M
 perl-mro                    x86_64 1.23-481.1.el9_6            appstream  28 k
 perl-overload               noarch 1.31-481.1.el9_6            appstream  45 k
 perl-overloading            noarch 0.02-481.1.el9_6            appstream  12 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 1.03-481.1.el9_6            appstream  11 k
 perl-vars                   noarch 1.05-481.1.el9_6            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 1.16.2-1.el9                appstream  14 k
 python-srpm-macros          noarch 3.9-54.el9                  appstream  18 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 4.16.1.3-39.el9             baseos    535 k
 rpm-build-libs              x86_64 4.16.1.3-39.el9             baseos     88 k
 rpm-libs                    x86_64 4.16.1.3-39.el9             baseos    307 k
 rpmautospec-rpm-macros      noarch 0.8.1-11.el9                epel       11 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 2:4.9-15.el9                baseos    1.2 M
 sqlite-libs                 x86_64 3.34.1-9.el9_7              baseos    642 k
 systemd-libs                x86_64 252-55.el9_7.7              baseos    676 k
 tzdata                      noarch 2025c-1.el9                 baseos    904 k
 util-linux-core             x86_64 2.37.4-21.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 1.5.5-1.el9                 baseos    468 k

Transaction Summary
================================================================================
Install  210 Packages

Total size: 70 M
Installed size: 222 M
Downloading Packages:
[SKIPPED] basesystem-11-13.el9.noarch.rpm: Already downloaded                  
[SKIPPED] cpio-2.13-16.el9.x86_64.rpm: Already downloaded                      
[SKIPPED] cracklib-2.9.6-27.el9.x86_64.rpm: Already downloaded                 
[SKIPPED] ed-1.14.2-12.el9.x86_64.rpm: Already downloaded                      
[SKIPPED] grep-3.6-5.el9.x86_64.rpm: Already downloaded                        
[SKIPPED] groff-base-1.22.4-10.el9.x86_64.rpm: Already downloaded              
[SKIPPED] info-6.7-15.el9.x86_64.rpm: Already downloaded                       
[SKIPPED] json-c-0.14-11.el9.x86_64.rpm: Already downloaded                    
[SKIPPED] libattr-2.5.1-3.el9.x86_64.rpm: Already downloaded                   
[SKIPPED] libcap-ng-0.8.2-7.el9.x86_64.rpm: Already downloaded                 
[SKIPPED] libgpg-error-1.42-5.el9.x86_64.rpm: Already downloaded               
[SKIPPED] libidn2-2.3.0-7.el9.x86_64.rpm: Already downloaded                   
[SKIPPED] libpsl-0.21.1-5.el9.x86_64.rpm: Already downloaded                   
[SKIPPED] libpwquality-1.4.4-8.el9.x86_64.rpm: Already downloaded              
[SKIPPED] libsigsegv-2.13-4.el9.x86_64.rpm: Already downloaded                 
[SKIPPED] libunistring-0.9.10-15.el9.x86_64.rpm: Already downloaded            
[SKIPPED] libutempter-1.2.1-6.el9.x86_64.rpm: Already downloaded               
[SKIPPED] libverto-0.3.2-3.el9.x86_64.rpm: Already downloaded                  
[SKIPPED] libxcrypt-4.4.18-3.el9.x86_64.rpm: Already downloaded                
[SKIPPED] lz4-libs-1.9.3-5.el9.x86_64.rpm: Already downloaded                  
[SKIPPED] mpfr-4.1.0-7.el9.x86_64.rpm: Already downloaded                      
[SKIPPED] popt-1.18-8.el9.x86_64.rpm: Already downloaded                       
[SKIPPED] publicsuffix-list-dafsa-20210518-3.el9.noarch.rpm: Already downloaded
[SKIPPED] readline-8.1-4.el9.x86_64.rpm: Already downloaded                    
[SKIPPED] sed-4.8-9.el9.x86_64.rpm: Already downloaded                         
[SKIPPED] cracklib-dicts-2.9.6-27.el9.x86_64.rpm: Already downloaded           
[SKIPPED] diffutils-3.7-12.el9.x86_64.rpm: Already downloaded                  
[SKIPPED] gawk-5.1.0-6.el9.x86_64.rpm: Already downloaded                      
[SKIPPED] xz-5.2.5-8.el9_0.x86_64.rpm: Already downloaded                      
[SKIPPED] xz-libs-5.2.5-8.el9_0.x86_64.rpm: Already downloaded                 
[SKIPPED] gzip-1.12-1.el9.x86_64.rpm: Already downloaded                       
[SKIPPED] keyutils-libs-1.6.3-1.el9.x86_64.rpm: Already downloaded             
[SKIPPED] libpkgconf-1.7.3-10.el9.x86_64.rpm: Already downloaded               
[SKIPPED] pkgconf-1.7.3-10.el9.x86_64.rpm: Already downloaded                  
[SKIPPED] pkgconf-m4-1.7.3-10.el9.noarch.rpm: Already downloaded               
[SKIPPED] pkgconf-pkg-config-1.7.3-10.el9.x86_64.rpm: Already downloaded       
[SKIPPED] zip-3.0-35.el9.x86_64.rpm: Already downloaded                        
[SKIPPED] gmp-6.2.0-13.el9.x86_64.rpm: Already downloaded                      
[SKIPPED] libffi-3.4.2-8.el9.x86_64.rpm: Already downloaded                    
[SKIPPED] lua-libs-5.4.4-4.el9.x86_64.rpm: Already downloaded                  
[SKIPPED] zlib-1.2.11-40.el9.x86_64.rpm: Already downloaded                    
[SKIPPED] bash-5.1.8-9.el9.x86_64.rpm: Already downloaded                      
[SKIPPED] file-5.39-16.el9.x86_64.rpm: Already downloaded                      
[SKIPPED] file-libs-5.39-16.el9.x86_64.rpm: Already downloaded                 
[SKIPPED] libacl-2.3.1-4.el9.x86_64.rpm: Already downloaded                    
[SKIPPED] setup-2.13.7-10.el9.noarch.rpm: Already downloaded                   
[SKIPPED] libevent-2.1.12-8.el9_4.x86_64.rpm: Already downloaded               
[SKIPPED] filesystem-3.16-5.el9.x86_64.rpm: Already downloaded                 
[SKIPPED] findutils-4.8.0-7.el9.x86_64.rpm: Already downloaded                 
[SKIPPED] gdbm-libs-1.23-1.el9.x86_64.rpm: Already downloaded                  
[SKIPPED] libeconf-0.4.1-4.el9.x86_64.rpm: Already downloaded                  
[SKIPPED] libgcrypt-1.10.0-11.el9.x86_64.rpm: Already downloaded               
[SKIPPED] libnghttp2-1.43.0-6.el9.x86_64.rpm: Already downloaded               
[SKIPPED] pcre-8.44-4.el9.x86_64.rpm: Already downloaded                       
[SKIPPED] pcre2-10.40-6.el9.x86_64.rpm: Already downloaded                     
[SKIPPED] pcre2-syntax-10.40-6.el9.noarch.rpm: Already downloaded              
[SKIPPED] bzip2-1.0.8-10.el9_5.x86_64.rpm: Already downloaded                  
[SKIPPED] bzip2-libs-1.0.8-10.el9_5.x86_64.rpm: Already downloaded             
[SKIPPED] libbrotli-1.0.9-7.el9_5.x86_64.rpm: Already downloaded               
[SKIPPED] p11-kit-0.25.3-3.el9_5.x86_64.rpm: Already downloaded                
[SKIPPED] p11-kit-trust-0.25.3-3.el9_5.x86_64.rpm: Already downloaded          
[SKIPPED] alternatives-1.24-2.el9.x86_64.rpm: Already downloaded               
[SKIPPED] coreutils-8.32-39.el9.x86_64.rpm: Already downloaded                 
[SKIPPED] coreutils-common-8.32-39.el9.x86_64.rpm: Already downloaded          
[SKIPPED] libblkid-2.37.4-21.el9.x86_64.rpm: Already downloaded                
[SKIPPED] libfdisk-2.37.4-21.el9.x86_64.rpm: Already downloaded                
[SKIPPED] libmount-2.37.4-21.el9.x86_64.rpm: Already downloaded                
[SKIPPED] libselinux-3.6-3.el9.x86_64.rpm: Already downloaded                  
[SKIPPED] libsemanage-3.6-5.el9_6.x86_64.rpm: Already downloaded               
[SKIPPED] libsmartcols-2.37.4-21.el9.x86_64.rpm: Already downloaded            
[SKIPPED] libtasn1-4.16.0-9.el9.x86_64.rpm: Already downloaded                 
[SKIPPED] libtool-ltdl-2.4.6-46.el9.x86_64.rpm: Already downloaded             
[SKIPPED] libuuid-2.37.4-21.el9.x86_64.rpm: Already downloaded                 
[SKIPPED] libzstd-1.5.5-1.el9.x86_64.rpm: Already downloaded                   
[SKIPPED] openldap-2.6.8-4.el9.x86_64.rpm: Already downloaded                  
[SKIPPED] util-linux-2.37.4-21.el9.x86_64.rpm: Already downloaded              
[SKIPPED] util-linux-core-2.37.4-21.el9.x86_64.rpm: Already downloaded         
[SKIPPED] zstd-1.5.5-1.el9.x86_64.rpm: Already downloaded                      
[SKIPPED] krb5-libs-1.21.1-8.el9_6.x86_64.rpm: Already downloaded              
[SKIPPED] libdb-5.3.28-57.el9_6.x86_64.rpm: Already downloaded                 
[SKIPPED] elfutils-0.193-1.el9.x86_64.rpm: Already downloaded                  
[SKIPPED] elfutils-libs-0.193-1.el9.x86_64.rpm: Already downloaded             
[SKIPPED] libarchive-3.5.3-6.el9_6.x86_64.rpm: Already downloaded              
[SKIPPED] libgcc-11.5.0-11.el9.x86_64.rpm: Already downloaded                  
[SKIPPED] ncurses-libs-6.2-12.20210508.el9.x86_64.rpm: Already downloaded      
[SKIPPED] pam-1.5.1-26.el9_6.x86_64.rpm: Already downloaded                    
[SKIPPED] rpm-build-libs-4.16.1.3-39.el9.x86_64.rpm: Already downloaded        
[SKIPPED] unzip-6.0-59.el9.x86_64.rpm: Already downloaded                      
[SKIPPED] which-2.21-30.el9_6.x86_64.rpm: Already downloaded                   
[SKIPPED] audit-libs-3.1.5-7.el9.x86_64.rpm: Already downloaded                
[SKIPPED] crypto-policies-20250905-1.git377cc42.el9_7.noarch.rpm: Already downloaded
[SKIPPED] curl-7.76.1-34.el9.x86_64.rpm: Already downloaded                    
[SKIPPED] cyrus-sasl-lib-2.1.27-22.el9.x86_64.rpm: Already downloaded          
[SKIPPED] elfutils-debuginfod-client-0.193-1.el9.x86_64.rpm: Already downloaded
[SKIPPED] elfutils-default-yama-scope-0.193-1.el9.noarch.rpm: Already downloaded
[SKIPPED] elfutils-libelf-0.193-1.el9.x86_64.rpm: Already downloaded           
[SKIPPED] libcap-2.48-10.el9.x86_64.rpm: Already downloaded                    
[SKIPPED] libcom_err-1.46.5-8.el9.x86_64.rpm: Already downloaded               
[SKIPPED] libcurl-7.76.1-34.el9.x86_64.rpm: Already downloaded                 
[SKIPPED] libgomp-11.5.0-11.el9.x86_64.rpm: Already downloaded                 
[SKIPPED] libsepol-3.6-3.el9.x86_64.rpm: Already downloaded                    
[SKIPPED] libstdc++-11.5.0-11.el9.x86_64.rpm: Already downloaded               
[SKIPPED] ncurses-6.2-12.20210508.el9.x86_64.rpm: Already downloaded           
[SKIPPED] ncurses-base-6.2-12.20210508.el9.noarch.rpm: Already downloaded      
[SKIPPED] openssl-fips-provider-3.0.7-8.el9.x86_64.rpm: Already downloaded     
[SKIPPED] openssl-fips-provider-so-3.0.7-8.el9.x86_64.rpm: Already downloaded  
[SKIPPED] rpm-4.16.1.3-39.el9.x86_64.rpm: Already downloaded                   
[SKIPPED] rpm-libs-4.16.1.3-39.el9.x86_64.rpm: Already downloaded              
[SKIPPED] shadow-utils-4.9-15.el9.x86_64.rpm: Already downloaded               
[SKIPPED] glibc-2.34-231.el9_7.2.x86_64.rpm: Already downloaded                
[SKIPPED] glibc-common-2.34-231.el9_7.2.x86_64.rpm: Already downloaded         
[SKIPPED] glibc-gconv-extra-2.34-231.el9_7.2.x86_64.rpm: Already downloaded    
[SKIPPED] glibc-minimal-langpack-2.34-231.el9_7.2.x86_64.rpm: Already downloaded
[SKIPPED] redhat-release-9.7-0.7.el9.x86_64.rpm: Already downloaded            
[SKIPPED] sqlite-libs-3.34.1-9.el9_7.x86_64.rpm: Already downloaded            
[SKIPPED] ca-certificates-2025.2.80_v9.0.305-91.el9.noarch.rpm: Already downloaded
[SKIPPED] libxml2-2.9.13-14.el9_7.x86_64.rpm: Already downloaded               
[SKIPPED] systemd-libs-252-55.el9_7.7.x86_64.rpm: Already downloaded           
[SKIPPED] tzdata-2025c-1.el9.noarch.rpm: Already downloaded                    
[SKIPPED] libssh-0.10.4-17.el9_7.x86_64.rpm: Already downloaded                
[SKIPPED] libssh-config-0.10.4-17.el9_7.noarch.rpm: Already downloaded         
[SKIPPED] binutils-2.35.2-67.el9_7.1.x86_64.rpm: Already downloaded            
[SKIPPED] binutils-gold-2.35.2-67.el9_7.1.x86_64.rpm: Already downloaded       
[SKIPPED] tar-1.34-9.el9_7.x86_64.rpm: Already downloaded                      
[SKIPPED] openssl-3.5.1-5.el9_7.x86_64.rpm: Already downloaded                 
[SKIPPED] openssl-libs-3.5.1-5.el9_7.x86_64.rpm: Already downloaded            
[SKIPPED] ghc-srpm-macros-1.5.0-6.el9.noarch.rpm: Already downloaded           
[SKIPPED] lua-srpm-macros-1-6.el9.noarch.rpm: Already downloaded               
[SKIPPED] perl-Data-Dumper-2.174-462.el9.x86_64.rpm: Already downloaded        
[SKIPPED] perl-Digest-MD5-2.58-4.el9.x86_64.rpm: Already downloaded            
[SKIPPED] perl-Encode-3.08-462.el9.x86_64.rpm: Already downloaded              
[SKIPPED] perl-Mozilla-CA-20200520-6.el9.noarch.rpm: Already downloaded        
[SKIPPED] perl-Pod-Simple-3.42-4.el9.noarch.rpm: Already downloaded            
[SKIPPED] perl-Term-Cap-1.17-460.el9.noarch.rpm: Already downloaded            
[SKIPPED] perl-Time-Local-1.300-7.el9.noarch.rpm: Already downloaded           
[SKIPPED] rust-srpm-macros-17-4.el9.noarch.rpm: Already downloaded             
[SKIPPED] perl-Pod-Escapes-1.07-460.el9.noarch.rpm: Already downloaded         
[SKIPPED] perl-Storable-3.21-460.el9.x86_64.rpm: Already downloaded            
[SKIPPED] perl-podlators-4.14-460.el9.noarch.rpm: Already downloaded           
[SKIPPED] perl-Exporter-5.74-461.el9.noarch.rpm: Already downloaded            
[SKIPPED] perl-File-Temp-0.231.100-4.el9.noarch.rpm: Already downloaded        
[SKIPPED] perl-Getopt-Long-2.52-4.el9.noarch.rpm: Already downloaded           
[SKIPPED] perl-MIME-Base64-3.16-4.el9.x86_64.rpm: Already downloaded           
[SKIPPED] perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch.rpm: Already downloaded 
[SKIPPED] perl-parent-0.238-460.el9.noarch.rpm: Already downloaded             
[SKIPPED] perl-srpm-macros-1-41.el9.noarch.rpm: Already downloaded             
[SKIPPED] openblas-srpm-macros-2-11.el9.noarch.rpm: Already downloaded         
[SKIPPED] perl-Digest-1.19-4.el9.noarch.rpm: Already downloaded                
[SKIPPED] perl-File-Path-2.18-4.el9.noarch.rpm: Already downloaded             
[SKIPPED] perl-IO-Socket-IP-0.41-5.el9.noarch.rpm: Already downloaded          
[SKIPPED] perl-Pod-Usage-2.01-4.el9.noarch.rpm: Already downloaded             
[SKIPPED] perl-Socket-2.031-4.el9.x86_64.rpm: Already downloaded               
[SKIPPED] perl-Term-ANSIColor-5.01-461.el9.noarch.rpm: Already downloaded      
[SKIPPED] perl-Text-ParseWords-3.30-460.el9.noarch.rpm: Already downloaded     
[SKIPPED] perl-URI-5.09-3.el9.noarch.rpm: Already downloaded                   
[SKIPPED] perl-constant-1.33-461.el9.noarch.rpm: Already downloaded            
[SKIPPED] fonts-srpm-macros-2.0.5-7.el9.1.noarch.rpm: Already downloaded       
[SKIPPED] ocaml-srpm-macros-6-6.el9.noarch.rpm: Already downloaded             
[SKIPPED] patch-2.7.6-16.el9.x86_64.rpm: Already downloaded                    
[SKIPPED] perl-Pod-Perldoc-3.28.01-461.el9.noarch.rpm: Already downloaded      
[SKIPPED] perl-libnet-3.13-4.el9.noarch.rpm: Already downloaded                
[SKIPPED] perl-Carp-1.50-460.el9.noarch.rpm: Already downloaded                
[SKIPPED] perl-PathTools-3.78-461.el9.x86_64.rpm: Already downloaded           
[SKIPPED] qt5-srpm-macros-5.15.9-1.el9.noarch.rpm: Already downloaded          
[SKIPPED] perl-HTTP-Tiny-0.076-462.el9.noarch.rpm: Already downloaded          
[SKIPPED] python-srpm-macros-3.9-54.el9.noarch.rpm: Already downloaded         
[SKIPPED] perl-IO-Socket-SSL-2.073-2.el9.noarch.rpm: Already downloaded        
[SKIPPED] perl-Scalar-List-Utils-1.56-462.el9.x86_64.rpm: Already downloaded   
[SKIPPED] pyproject-srpm-macros-1.16.2-1.el9.noarch.rpm: Already downloaded    
[SKIPPED] perl-AutoLoader-5.74-481.1.el9_6.noarch.rpm: Already downloaded      
[SKIPPED] perl-B-1.80-481.1.el9_6.x86_64.rpm: Already downloaded               
[SKIPPED] perl-Class-Struct-0.66-481.1.el9_6.noarch.rpm: Already downloaded    
[SKIPPED] perl-Errno-1.30-481.1.el9_6.x86_64.rpm: Already downloaded           
[SKIPPED] perl-Fcntl-1.13-481.1.el9_6.x86_64.rpm: Already downloaded           
[SKIPPED] perl-File-Basename-2.85-481.1.el9_6.noarch.rpm: Already downloaded   
[SKIPPED] perl-File-stat-1.09-481.1.el9_6.noarch.rpm: Already downloaded       
[SKIPPED] perl-FileHandle-2.03-481.1.el9_6.noarch.rpm: Already downloaded      
[SKIPPED] perl-Getopt-Std-1.12-481.1.el9_6.noarch.rpm: Already downloaded      
[SKIPPED] perl-IO-1.43-481.1.el9_6.x86_64.rpm: Already downloaded              
[SKIPPED] perl-IPC-Open3-1.21-481.1.el9_6.noarch.rpm: Already downloaded       
[SKIPPED] perl-POSIX-1.94-481.1.el9_6.x86_64.rpm: Already downloaded           
[SKIPPED] perl-SelectSaver-1.02-481.1.el9_6.noarch.rpm: Already downloaded     
[SKIPPED] perl-Symbol-1.08-481.1.el9_6.noarch.rpm: Already downloaded          
[SKIPPED] perl-base-2.27-481.1.el9_6.noarch.rpm: Already downloaded            
[SKIPPED] perl-if-0.60.800-481.1.el9_6.noarch.rpm: Already downloaded          
[SKIPPED] perl-interpreter-5.32.1-481.1.el9_6.x86_64.rpm: Already downloaded   
[SKIPPED] perl-libs-5.32.1-481.1.el9_6.x86_64.rpm: Already downloaded          
[SKIPPED] perl-mro-1.23-481.1.el9_6.x86_64.rpm: Already downloaded             
[SKIPPED] perl-overload-1.31-481.1.el9_6.noarch.rpm: Already downloaded        
[SKIPPED] perl-overloading-0.02-481.1.el9_6.noarch.rpm: Already downloaded     
[SKIPPED] perl-subs-1.03-481.1.el9_6.noarch.rpm: Already downloaded            
[SKIPPED] perl-vars-1.05-481.1.el9_6.noarch.rpm: Already downloaded            
[SKIPPED] dwz-0.16-1.el9.x86_64.rpm: Already downloaded                        
[SKIPPED] debugedit-5.0-11.el9.x86_64.rpm: Already downloaded                  
[SKIPPED] efi-srpm-macros-6-4.el9.noarch.rpm: Already downloaded               
[SKIPPED] gdb-minimal-16.3-2.el9.x86_64.rpm: Already downloaded                
[SKIPPED] kernel-srpm-macros-1.0-14.el9.noarch.rpm: Already downloaded         
[SKIPPED] perl-Net-SSLeay-1.94-3.el9.x86_64.rpm: Already downloaded            
[SKIPPED] redhat-rpm-config-210-1.el9.noarch.rpm: Already downloaded           
[SKIPPED] rpm-build-4.16.1.3-39.el9.x86_64.rpm: Already downloaded             
[SKIPPED] go-srpm-macros-3.6.0-12.el9_7.noarch.rpm: Already downloaded         
[SKIPPED] ansible-srpm-macros-1-16.el9.noarch.rpm: Already downloaded          
[SKIPPED] epel-rpm-macros-9-17.el9.noarch.rpm: Already downloaded              
[SKIPPED] forge-srpm-macros-0.4.0-1.el9.noarch.rpm: Already downloaded         
[SKIPPED] fpc-srpm-macros-1.3-7.el9.noarch.rpm: Already downloaded             
[SKIPPED] ghc-srpm-macros-epel-1.9.1-1.el9.noarch.rpm: Already downloaded      
[SKIPPED] go-srpm-macros-epel-3.8.0-1.el9.noarch.rpm: Already downloaded       
[SKIPPED] qt6-srpm-macros-6.6.2-1.el9.noarch.rpm: Already downloaded           
[SKIPPED] rpmautospec-rpm-macros-0.8.1-11.el9.noarch.rpm: Already downloaded   
[SKIPPED] rust-srpm-macros-epel-26.3-1.el9.noarch.rpm: Already downloaded      
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) <security@redhat.com>"
 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) <security@redhat.com>"
 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) <epel@fedoraproject.org>"
 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-3.16-5.el9.x86_64                           1/1 
  Preparing        :                                                        1/1 
  Installing       : rust-srpm-macros-17-4.el9.noarch                     1/210 
  Installing       : redhat-release-9.7-0.7.el9.x86_64                    2/210 
  Installing       : setup-2.13.7-10.el9.noarch                           3/210 
warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.13.7-10.el9.noarch                           3/210 
  Installing       : filesystem-3.16-5.el9.x86_64                         4/210 
  Installing       : basesystem-11-13.el9.noarch                          5/210 
  Installing       : rust-srpm-macros-epel-26.3-1.el9.noarch              6/210 
  Installing       : qt6-srpm-macros-6.6.2-1.el9.noarch                   7/210 
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  Verifying        : zip-3.0-35.el9.x86_64                               37/210 
  Verifying        : gmp-1:6.2.0-13.el9.x86_64                           38/210 
  Verifying        : libffi-3.4.2-8.el9.x86_64                           39/210 
  Verifying        : lua-libs-5.4.4-4.el9.x86_64                         40/210 
  Verifying        : zlib-1.2.11-40.el9.x86_64                           41/210 
  Verifying        : bash-5.1.8-9.el9.x86_64                             42/210 
  Verifying        : file-5.39-16.el9.x86_64                             43/210 
  Verifying        : file-libs-5.39-16.el9.x86_64                        44/210 
  Verifying        : libacl-2.3.1-4.el9.x86_64                           45/210 
  Verifying        : setup-2.13.7-10.el9.noarch                          46/210 
  Verifying        : libevent-2.1.12-8.el9_4.x86_64                      47/210 
  Verifying        : filesystem-3.16-5.el9.x86_64                        48/210 
  Verifying        : findutils-1:4.8.0-7.el9.x86_64                      49/210 
  Verifying        : gdbm-libs-1:1.23-1.el9.x86_64                       50/210 
  Verifying        : libeconf-0.4.1-4.el9.x86_64                         51/210 
  Verifying        : libgcrypt-1.10.0-11.el9.x86_64                      52/210 
  Verifying        : libnghttp2-1.43.0-6.el9.x86_64                      53/210 
  Verifying        : pcre-8.44-4.el9.x86_64                              54/210 
  Verifying        : pcre2-10.40-6.el9.x86_64                            55/210 
  Verifying        : pcre2-syntax-10.40-6.el9.noarch                     56/210 
  Verifying        : bzip2-1.0.8-10.el9_5.x86_64                         57/210 
  Verifying        : bzip2-libs-1.0.8-10.el9_5.x86_64                    58/210 
  Verifying        : libbrotli-1.0.9-7.el9_5.x86_64                      59/210 
  Verifying        : p11-kit-0.25.3-3.el9_5.x86_64                       60/210 
  Verifying        : p11-kit-trust-0.25.3-3.el9_5.x86_64                 61/210 
  Verifying        : alternatives-1.24-2.el9.x86_64                      62/210 
  Verifying        : coreutils-8.32-39.el9.x86_64                        63/210 
  Verifying        : coreutils-common-8.32-39.el9.x86_64                 64/210 
  Verifying        : libblkid-2.37.4-21.el9.x86_64                       65/210 
  Verifying        : libfdisk-2.37.4-21.el9.x86_64                       66/210 
  Verifying        : libmount-2.37.4-21.el9.x86_64                       67/210 
  Verifying        : libselinux-3.6-3.el9.x86_64                         68/210 
  Verifying        : libsemanage-3.6-5.el9_6.x86_64                      69/210 
  Verifying        : libsmartcols-2.37.4-21.el9.x86_64                   70/210 
  Verifying        : libtasn1-4.16.0-9.el9.x86_64                        71/210 
  Verifying        : libtool-ltdl-2.4.6-46.el9.x86_64                    72/210 
  Verifying        : libuuid-2.37.4-21.el9.x86_64                        73/210 
  Verifying        : libzstd-1.5.5-1.el9.x86_64                          74/210 
  Verifying        : openldap-2.6.8-4.el9.x86_64                         75/210 
  Verifying        : util-linux-2.37.4-21.el9.x86_64                     76/210 
  Verifying        : util-linux-core-2.37.4-21.el9.x86_64                77/210 
  Verifying        : zstd-1.5.5-1.el9.x86_64                             78/210 
  Verifying        : krb5-libs-1.21.1-8.el9_6.x86_64                     79/210 
  Verifying        : libdb-5.3.28-57.el9_6.x86_64                        80/210 
  Verifying        : elfutils-0.193-1.el9.x86_64                         81/210 
  Verifying        : elfutils-libs-0.193-1.el9.x86_64                    82/210 
  Verifying        : libarchive-3.5.3-6.el9_6.x86_64                     83/210 
  Verifying        : libgcc-11.5.0-11.el9.x86_64                         84/210 
  Verifying        : ncurses-libs-6.2-12.20210508.el9.x86_64             85/210 
  Verifying        : pam-1.5.1-26.el9_6.x86_64                           86/210 
  Verifying        : rpm-build-libs-4.16.1.3-39.el9.x86_64               87/210 
  Verifying        : unzip-6.0-59.el9.x86_64                             88/210 
  Verifying        : which-2.21-30.el9_6.x86_64                          89/210 
  Verifying        : audit-libs-3.1.5-7.el9.x86_64                       90/210 
  Verifying        : crypto-policies-20250905-1.git377cc42.el9_7.noar    91/210 
  Verifying        : curl-7.76.1-34.el9.x86_64                           92/210 
  Verifying        : cyrus-sasl-lib-2.1.27-22.el9.x86_64                 93/210 
  Verifying        : elfutils-debuginfod-client-0.193-1.el9.x86_64       94/210 
  Verifying        : elfutils-default-yama-scope-0.193-1.el9.noarch      95/210 
  Verifying        : elfutils-libelf-0.193-1.el9.x86_64                  96/210 
  Verifying        : libcap-2.48-10.el9.x86_64                           97/210 
  Verifying        : libcom_err-1.46.5-8.el9.x86_64                      98/210 
  Verifying        : libcurl-7.76.1-34.el9.x86_64                        99/210 
  Verifying        : libgomp-11.5.0-11.el9.x86_64                       100/210 
  Verifying        : libsepol-3.6-3.el9.x86_64                          101/210 
  Verifying        : libstdc++-11.5.0-11.el9.x86_64                     102/210 
  Verifying        : ncurses-6.2-12.20210508.el9.x86_64                 103/210 
  Verifying        : ncurses-base-6.2-12.20210508.el9.noarch            104/210 
  Verifying        : openssl-fips-provider-3.0.7-8.el9.x86_64           105/210 
  Verifying        : openssl-fips-provider-so-3.0.7-8.el9.x86_64        106/210 
  Verifying        : rpm-4.16.1.3-39.el9.x86_64                         107/210 
  Verifying        : rpm-libs-4.16.1.3-39.el9.x86_64                    108/210 
  Verifying        : shadow-utils-2:4.9-15.el9.x86_64                   109/210 
  Verifying        : glibc-2.34-231.el9_7.2.x86_64                      110/210 
  Verifying        : glibc-common-2.34-231.el9_7.2.x86_64               111/210 
  Verifying        : glibc-gconv-extra-2.34-231.el9_7.2.x86_64          112/210 
  Verifying        : glibc-minimal-langpack-2.34-231.el9_7.2.x86_64     113/210 
  Verifying        : redhat-release-9.7-0.7.el9.x86_64                  114/210 
  Verifying        : sqlite-libs-3.34.1-9.el9_7.x86_64                  115/210 
  Verifying        : ca-certificates-2025.2.80_v9.0.305-91.el9.noarch   116/210 
  Verifying        : libxml2-2.9.13-14.el9_7.x86_64                     117/210 
  Verifying        : systemd-libs-252-55.el9_7.7.x86_64                 118/210 
  Verifying        : tzdata-2025c-1.el9.noarch                          119/210 
  Verifying        : libssh-0.10.4-17.el9_7.x86_64                      120/210 
  Verifying        : libssh-config-0.10.4-17.el9_7.noarch               121/210 
  Verifying        : binutils-2.35.2-67.el9_7.1.x86_64                  122/210 
  Verifying        : binutils-gold-2.35.2-67.el9_7.1.x86_64             123/210 
  Verifying        : tar-2:1.34-9.el9_7.x86_64                          124/210 
  Verifying        : openssl-1:3.5.1-5.el9_7.x86_64                     125/210 
  Verifying        : openssl-libs-1:3.5.1-5.el9_7.x86_64                126/210 
  Verifying        : ghc-srpm-macros-1.5.0-6.el9.noarch                 127/210 
  Verifying        : lua-srpm-macros-1-6.el9.noarch                     128/210 
  Verifying        : perl-Data-Dumper-2.174-462.el9.x86_64              129/210 
  Verifying        : perl-Digest-MD5-2.58-4.el9.x86_64                  130/210 
  Verifying        : perl-Encode-4:3.08-462.el9.x86_64                  131/210 
  Verifying        : perl-Mozilla-CA-20200520-6.el9.noarch              132/210 
  Verifying        : perl-Pod-Simple-1:3.42-4.el9.noarch                133/210 
  Verifying        : perl-Term-Cap-1.17-460.el9.noarch                  134/210 
  Verifying        : perl-Time-Local-2:1.300-7.el9.noarch               135/210 
  Verifying        : rust-srpm-macros-17-4.el9.noarch                   136/210 
  Verifying        : perl-Pod-Escapes-1:1.07-460.el9.noarch             137/210 
  Verifying        : perl-Storable-1:3.21-460.el9.x86_64                138/210 
  Verifying        : perl-podlators-1:4.14-460.el9.noarch               139/210 
  Verifying        : perl-Exporter-5.74-461.el9.noarch                  140/210 
  Verifying        : perl-File-Temp-1:0.231.100-4.el9.noarch            141/210 
  Verifying        : perl-Getopt-Long-1:2.52-4.el9.noarch               142/210 
  Verifying        : perl-MIME-Base64-3.16-4.el9.x86_64                 143/210 
  Verifying        : perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch       144/210 
  Verifying        : perl-parent-1:0.238-460.el9.noarch                 145/210 
  Verifying        : perl-srpm-macros-1-41.el9.noarch                   146/210 
  Verifying        : openblas-srpm-macros-2-11.el9.noarch               147/210 
  Verifying        : perl-Digest-1.19-4.el9.noarch                      148/210 
  Verifying        : perl-File-Path-2.18-4.el9.noarch                   149/210 
  Verifying        : perl-IO-Socket-IP-0.41-5.el9.noarch                150/210 
  Verifying        : perl-Pod-Usage-4:2.01-4.el9.noarch                 151/210 
  Verifying        : perl-Socket-4:2.031-4.el9.x86_64                   152/210 
  Verifying        : perl-Term-ANSIColor-5.01-461.el9.noarch            153/210 
  Verifying        : perl-Text-ParseWords-3.30-460.el9.noarch           154/210 
  Verifying        : perl-URI-5.09-3.el9.noarch                         155/210 
  Verifying        : perl-constant-1.33-461.el9.noarch                  156/210 
  Verifying        : fonts-srpm-macros-1:2.0.5-7.el9.1.noarch           157/210 
  Verifying        : ocaml-srpm-macros-6-6.el9.noarch                   158/210 
  Verifying        : patch-2.7.6-16.el9.x86_64                          159/210 
  Verifying        : perl-Pod-Perldoc-3.28.01-461.el9.noarch            160/210 
  Verifying        : perl-libnet-3.13-4.el9.noarch                      161/210 
  Verifying        : perl-Carp-1.50-460.el9.noarch                      162/210 
  Verifying        : perl-PathTools-3.78-461.el9.x86_64                 163/210 
  Verifying        : qt5-srpm-macros-5.15.9-1.el9.noarch                164/210 
  Verifying        : perl-HTTP-Tiny-0.076-462.el9.noarch                165/210 
  Verifying        : python-srpm-macros-3.9-54.el9.noarch               166/210 
  Verifying        : perl-IO-Socket-SSL-2.073-2.el9.noarch              167/210 
  Verifying        : perl-Scalar-List-Utils-4:1.56-462.el9.x86_64       168/210 
  Verifying        : pyproject-srpm-macros-1.16.2-1.el9.noarch          169/210 
  Verifying        : perl-AutoLoader-5.74-481.1.el9_6.noarch            170/210 
  Verifying        : perl-B-1.80-481.1.el9_6.x86_64                     171/210 
  Verifying        : perl-Class-Struct-0.66-481.1.el9_6.noarch          172/210 
  Verifying        : perl-Errno-1.30-481.1.el9_6.x86_64                 173/210 
  Verifying        : perl-Fcntl-1.13-481.1.el9_6.x86_64                 174/210 
  Verifying        : perl-File-Basename-2.85-481.1.el9_6.noarch         175/210 
  Verifying        : perl-File-stat-1.09-481.1.el9_6.noarch             176/210 
  Verifying        : perl-FileHandle-2.03-481.1.el9_6.noarch            177/210 
  Verifying        : perl-Getopt-Std-1.12-481.1.el9_6.noarch            178/210 
  Verifying        : perl-IO-1.43-481.1.el9_6.x86_64                    179/210 
  Verifying        : perl-IPC-Open3-1.21-481.1.el9_6.noarch             180/210 
  Verifying        : perl-POSIX-1.94-481.1.el9_6.x86_64                 181/210 
  Verifying        : perl-SelectSaver-1.02-481.1.el9_6.noarch           182/210 
  Verifying        : perl-Symbol-1.08-481.1.el9_6.noarch                183/210 
  Verifying        : perl-base-2.27-481.1.el9_6.noarch                  184/210 
  Verifying        : perl-if-0.60.800-481.1.el9_6.noarch                185/210 
  Verifying        : perl-interpreter-4:5.32.1-481.1.el9_6.x86_64       186/210 
  Verifying        : perl-libs-4:5.32.1-481.1.el9_6.x86_64              187/210 
  Verifying        : perl-mro-1.23-481.1.el9_6.x86_64                   188/210 
  Verifying        : perl-overload-1.31-481.1.el9_6.noarch              189/210 
  Verifying        : perl-overloading-0.02-481.1.el9_6.noarch           190/210 
  Verifying        : perl-subs-1.03-481.1.el9_6.noarch                  191/210 
  Verifying        : perl-vars-1.05-481.1.el9_6.noarch                  192/210 
  Verifying        : dwz-0.16-1.el9.x86_64                              193/210 
  Verifying        : debugedit-5.0-11.el9.x86_64                        194/210 
  Verifying        : efi-srpm-macros-6-4.el9.noarch                     195/210 
  Verifying        : gdb-minimal-16.3-2.el9.x86_64                      196/210 
  Verifying        : kernel-srpm-macros-1.0-14.el9.noarch               197/210 
  Verifying        : perl-Net-SSLeay-1.94-3.el9.x86_64                  198/210 
  Verifying        : redhat-rpm-config-210-1.el9.noarch                 199/210 
  Verifying        : rpm-build-4.16.1.3-39.el9.x86_64                   200/210 
  Verifying        : go-srpm-macros-3.6.0-12.el9_7.noarch               201/210 
  Verifying        : ansible-srpm-macros-1-16.el9.noarch                202/210 
  Verifying        : epel-rpm-macros-9-17.el9.noarch                    203/210 
  Verifying        : forge-srpm-macros-0.4.0-1.el9.noarch               204/210 
  Verifying        : fpc-srpm-macros-1.3-7.el9.noarch                   205/210 
  Verifying        : ghc-srpm-macros-epel-1.9.1-1.el9.noarch            206/210 
  Verifying        : go-srpm-macros-epel-3.8.0-1.el9.noarch             207/210 
  Verifying        : qt6-srpm-macros-6.6.2-1.el9.noarch                 208/210 
  Verifying        : rpmautospec-rpm-macros-0.8.1-11.el9.noarch         209/210 
  Verifying        : rust-srpm-macros-epel-26.3-1.el9.noarch            210/210 
Installed products updated.

Installed:
  alternatives-1.24-2.el9.x86_64                                                
  ansible-srpm-macros-1-16.el9.noarch                                           
  audit-libs-3.1.5-7.el9.x86_64                                                 
  basesystem-11-13.el9.noarch                                                   
  bash-5.1.8-9.el9.x86_64                                                       
  binutils-2.35.2-67.el9_7.1.x86_64                                             
  binutils-gold-2.35.2-67.el9_7.1.x86_64                                        
  bzip2-1.0.8-10.el9_5.x86_64                                                   
  bzip2-libs-1.0.8-10.el9_5.x86_64                                              
  ca-certificates-2025.2.80_v9.0.305-91.el9.noarch                              
  coreutils-8.32-39.el9.x86_64                                                  
  coreutils-common-8.32-39.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-20250905-1.git377cc42.el9_7.noarch                            
  curl-7.76.1-34.el9.x86_64                                                     
  cyrus-sasl-lib-2.1.27-22.el9.x86_64                                           
  debugedit-5.0-11.el9.x86_64                                                   
  diffutils-3.7-12.el9.x86_64                                                   
  dwz-0.16-1.el9.x86_64                                                         
  ed-1.14.2-12.el9.x86_64                                                       
  efi-srpm-macros-6-4.el9.noarch                                                
  elfutils-0.193-1.el9.x86_64                                                   
  elfutils-debuginfod-client-0.193-1.el9.x86_64                                 
  elfutils-default-yama-scope-0.193-1.el9.noarch                                
  elfutils-libelf-0.193-1.el9.x86_64                                            
  elfutils-libs-0.193-1.el9.x86_64                                              
  epel-rpm-macros-9-17.el9.noarch                                               
  file-5.39-16.el9.x86_64                                                       
  file-libs-5.39-16.el9.x86_64                                                  
  filesystem-3.16-5.el9.x86_64                                                  
  findutils-1:4.8.0-7.el9.x86_64                                                
  fonts-srpm-macros-1:2.0.5-7.el9.1.noarch                                      
  forge-srpm-macros-0.4.0-1.el9.noarch                                          
  fpc-srpm-macros-1.3-7.el9.noarch                                              
  gawk-5.1.0-6.el9.x86_64                                                       
  gdb-minimal-16.3-2.el9.x86_64                                                 
  gdbm-libs-1:1.23-1.el9.x86_64                                                 
  ghc-srpm-macros-1.5.0-6.el9.noarch                                            
  ghc-srpm-macros-epel-1.9.1-1.el9.noarch                                       
  glibc-2.34-231.el9_7.2.x86_64                                                 
  glibc-common-2.34-231.el9_7.2.x86_64                                          
  glibc-gconv-extra-2.34-231.el9_7.2.x86_64                                     
  glibc-minimal-langpack-2.34-231.el9_7.2.x86_64                                
  gmp-1:6.2.0-13.el9.x86_64                                                     
  go-srpm-macros-3.6.0-12.el9_7.noarch                                          
  go-srpm-macros-epel-3.8.0-1.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                                                        
  json-c-0.14-11.el9.x86_64                                                     
  kernel-srpm-macros-1.0-14.el9.noarch                                          
  keyutils-libs-1.6.3-1.el9.x86_64                                              
  krb5-libs-1.21.1-8.el9_6.x86_64                                               
  libacl-2.3.1-4.el9.x86_64                                                     
  libarchive-3.5.3-6.el9_6.x86_64                                               
  libattr-2.5.1-3.el9.x86_64                                                    
  libblkid-2.37.4-21.el9.x86_64                                                 
  libbrotli-1.0.9-7.el9_5.x86_64                                                
  libcap-2.48-10.el9.x86_64                                                     
  libcap-ng-0.8.2-7.el9.x86_64                                                  
  libcom_err-1.46.5-8.el9.x86_64                                                
  libcurl-7.76.1-34.el9.x86_64                                                  
  libdb-5.3.28-57.el9_6.x86_64                                                  
  libeconf-0.4.1-4.el9.x86_64                                                   
  libevent-2.1.12-8.el9_4.x86_64                                                
  libfdisk-2.37.4-21.el9.x86_64                                                 
  libffi-3.4.2-8.el9.x86_64                                                     
  libgcc-11.5.0-11.el9.x86_64                                                   
  libgcrypt-1.10.0-11.el9.x86_64                                                
  libgomp-11.5.0-11.el9.x86_64                                                  
  libgpg-error-1.42-5.el9.x86_64                                                
  libidn2-2.3.0-7.el9.x86_64                                                    
  libmount-2.37.4-21.el9.x86_64                                                 
  libnghttp2-1.43.0-6.el9.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-3.6-3.el9.x86_64                                                   
  libsemanage-3.6-5.el9_6.x86_64                                                
  libsepol-3.6-3.el9.x86_64                                                     
  libsigsegv-2.13-4.el9.x86_64                                                  
  libsmartcols-2.37.4-21.el9.x86_64                                             
  libssh-0.10.4-17.el9_7.x86_64                                                 
  libssh-config-0.10.4-17.el9_7.noarch                                          
  libstdc++-11.5.0-11.el9.x86_64                                                
  libtasn1-4.16.0-9.el9.x86_64                                                  
  libtool-ltdl-2.4.6-46.el9.x86_64                                              
  libunistring-0.9.10-15.el9.x86_64                                             
  libutempter-1.2.1-6.el9.x86_64                                                
  libuuid-2.37.4-21.el9.x86_64                                                  
  libverto-0.3.2-3.el9.x86_64                                                   
  libxcrypt-4.4.18-3.el9.x86_64                                                 
  libxml2-2.9.13-14.el9_7.x86_64                                                
  libzstd-1.5.5-1.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-6.2-12.20210508.el9.x86_64                                            
  ncurses-base-6.2-12.20210508.el9.noarch                                       
  ncurses-libs-6.2-12.20210508.el9.x86_64                                       
  ocaml-srpm-macros-6-6.el9.noarch                                              
  openblas-srpm-macros-2-11.el9.noarch                                          
  openldap-2.6.8-4.el9.x86_64                                                   
  openssl-1:3.5.1-5.el9_7.x86_64                                                
  openssl-fips-provider-3.0.7-8.el9.x86_64                                      
  openssl-fips-provider-so-3.0.7-8.el9.x86_64                                   
  openssl-libs-1:3.5.1-5.el9_7.x86_64                                           
  p11-kit-0.25.3-3.el9_5.x86_64                                                 
  p11-kit-trust-0.25.3-3.el9_5.x86_64                                           
  pam-1.5.1-26.el9_6.x86_64                                                     
  patch-2.7.6-16.el9.x86_64                                                     
  pcre-8.44-4.el9.x86_64                                                        
  pcre2-10.40-6.el9.x86_64                                                      
  pcre2-syntax-10.40-6.el9.noarch                                               
  perl-AutoLoader-5.74-481.1.el9_6.noarch                                       
  perl-B-1.80-481.1.el9_6.x86_64                                                
  perl-Carp-1.50-460.el9.noarch                                                 
  perl-Class-Struct-0.66-481.1.el9_6.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-1.30-481.1.el9_6.x86_64                                            
  perl-Exporter-5.74-461.el9.noarch                                             
  perl-Fcntl-1.13-481.1.el9_6.x86_64                                            
  perl-File-Basename-2.85-481.1.el9_6.noarch                                    
  perl-File-Path-2.18-4.el9.noarch                                              
  perl-File-Temp-1:0.231.100-4.el9.noarch                                       
  perl-File-stat-1.09-481.1.el9_6.noarch                                        
  perl-FileHandle-2.03-481.1.el9_6.noarch                                       
  perl-Getopt-Long-1:2.52-4.el9.noarch                                          
  perl-Getopt-Std-1.12-481.1.el9_6.noarch                                       
  perl-HTTP-Tiny-0.076-462.el9.noarch                                           
  perl-IO-1.43-481.1.el9_6.x86_64                                               
  perl-IO-Socket-IP-0.41-5.el9.noarch                                           
  perl-IO-Socket-SSL-2.073-2.el9.noarch                                         
  perl-IPC-Open3-1.21-481.1.el9_6.noarch                                        
  perl-MIME-Base64-3.16-4.el9.x86_64                                            
  perl-Mozilla-CA-20200520-6.el9.noarch                                         
  perl-Net-SSLeay-1.94-3.el9.x86_64                                             
  perl-POSIX-1.94-481.1.el9_6.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-4:1.56-462.el9.x86_64                                  
  perl-SelectSaver-1.02-481.1.el9_6.noarch                                      
  perl-Socket-4:2.031-4.el9.x86_64                                              
  perl-Storable-1:3.21-460.el9.x86_64                                           
  perl-Symbol-1.08-481.1.el9_6.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-2.27-481.1.el9_6.noarch                                             
  perl-constant-1.33-461.el9.noarch                                             
  perl-if-0.60.800-481.1.el9_6.noarch                                           
  perl-interpreter-4:5.32.1-481.1.el9_6.x86_64                                  
  perl-libnet-3.13-4.el9.noarch                                                 
  perl-libs-4:5.32.1-481.1.el9_6.x86_64                                         
  perl-mro-1.23-481.1.el9_6.x86_64                                              
  perl-overload-1.31-481.1.el9_6.noarch                                         
  perl-overloading-0.02-481.1.el9_6.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-1.03-481.1.el9_6.noarch                                             
  perl-vars-1.05-481.1.el9_6.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-1.16.2-1.el9.noarch                                     
  python-srpm-macros-3.9-54.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-9.7-0.7.el9.x86_64                                             
  redhat-rpm-config-210-1.el9.noarch                                            
  rpm-4.16.1.3-39.el9.x86_64                                                    
  rpm-build-4.16.1.3-39.el9.x86_64                                              
  rpm-build-libs-4.16.1.3-39.el9.x86_64                                         
  rpm-libs-4.16.1.3-39.el9.x86_64                                               
  rpmautospec-rpm-macros-0.8.1-11.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-2:4.9-15.el9.x86_64                                              
  sqlite-libs-3.34.1-9.el9_7.x86_64                                             
  systemd-libs-252-55.el9_7.7.x86_64                                            
  tar-2:1.34-9.el9_7.x86_64                                                     
  tzdata-2025c-1.el9.noarch                                                     
  unzip-6.0-59.el9.x86_64                                                       
  util-linux-2.37.4-21.el9.x86_64                                               
  util-linux-core-2.37.4-21.el9.x86_64                                          
  which-2.21-30.el9_6.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-1.5.5-1.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-1.24-2.el9.x86_64
ansible-srpm-macros-1-16.el9.noarch
audit-libs-3.1.5-7.el9.x86_64
basesystem-11-13.el9.noarch
bash-5.1.8-9.el9.x86_64
binutils-2.35.2-67.el9_7.1.x86_64
binutils-gold-2.35.2-67.el9_7.1.x86_64
bzip2-1.0.8-10.el9_5.x86_64
bzip2-libs-1.0.8-10.el9_5.x86_64
ca-certificates-2025.2.80_v9.0.305-91.el9.noarch
coreutils-8.32-39.el9.x86_64
coreutils-common-8.32-39.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-20250905-1.git377cc42.el9_7.noarch
curl-7.76.1-34.el9.x86_64
cyrus-sasl-lib-2.1.27-22.el9.x86_64
debugedit-5.0-11.el9.x86_64
diffutils-3.7-12.el9.x86_64
dwz-0.16-1.el9.x86_64
ed-1.14.2-12.el9.x86_64
efi-srpm-macros-6-4.el9.noarch
elfutils-0.193-1.el9.x86_64
elfutils-debuginfod-client-0.193-1.el9.x86_64
elfutils-default-yama-scope-0.193-1.el9.noarch
elfutils-libelf-0.193-1.el9.x86_64
elfutils-libs-0.193-1.el9.x86_64
epel-rpm-macros-9-17.el9.noarch
file-5.39-16.el9.x86_64
file-libs-5.39-16.el9.x86_64
filesystem-3.16-5.el9.x86_64
findutils-4.8.0-7.el9.x86_64
fonts-srpm-macros-2.0.5-7.el9.1.noarch
forge-srpm-macros-0.4.0-1.el9.noarch
fpc-srpm-macros-1.3-7.el9.noarch
gawk-5.1.0-6.el9.x86_64
gdb-minimal-16.3-2.el9.x86_64
gdbm-libs-1.23-1.el9.x86_64
ghc-srpm-macros-1.5.0-6.el9.noarch
ghc-srpm-macros-epel-1.9.1-1.el9.noarch
glibc-2.34-231.el9_7.2.x86_64
glibc-common-2.34-231.el9_7.2.x86_64
glibc-gconv-extra-2.34-231.el9_7.2.x86_64
glibc-minimal-langpack-2.34-231.el9_7.2.x86_64
gmp-6.2.0-13.el9.x86_64
go-srpm-macros-3.6.0-12.el9_7.noarch
go-srpm-macros-epel-3.8.0-1.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
json-c-0.14-11.el9.x86_64
kernel-srpm-macros-1.0-14.el9.noarch
keyutils-libs-1.6.3-1.el9.x86_64
krb5-libs-1.21.1-8.el9_6.x86_64
libacl-2.3.1-4.el9.x86_64
libarchive-3.5.3-6.el9_6.x86_64
libattr-2.5.1-3.el9.x86_64
libblkid-2.37.4-21.el9.x86_64
libbrotli-1.0.9-7.el9_5.x86_64
libcap-2.48-10.el9.x86_64
libcap-ng-0.8.2-7.el9.x86_64
libcom_err-1.46.5-8.el9.x86_64
libcurl-7.76.1-34.el9.x86_64
libdb-5.3.28-57.el9_6.x86_64
libeconf-0.4.1-4.el9.x86_64
libevent-2.1.12-8.el9_4.x86_64
libfdisk-2.37.4-21.el9.x86_64
libffi-3.4.2-8.el9.x86_64
libgcc-11.5.0-11.el9.x86_64
libgcrypt-1.10.0-11.el9.x86_64
libgomp-11.5.0-11.el9.x86_64
libgpg-error-1.42-5.el9.x86_64
libidn2-2.3.0-7.el9.x86_64
libmount-2.37.4-21.el9.x86_64
libnghttp2-1.43.0-6.el9.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-3.6-3.el9.x86_64
libsemanage-3.6-5.el9_6.x86_64
libsepol-3.6-3.el9.x86_64
libsigsegv-2.13-4.el9.x86_64
libsmartcols-2.37.4-21.el9.x86_64
libssh-0.10.4-17.el9_7.x86_64
libssh-config-0.10.4-17.el9_7.noarch
libstdc++-11.5.0-11.el9.x86_64
libtasn1-4.16.0-9.el9.x86_64
libtool-ltdl-2.4.6-46.el9.x86_64
libunistring-0.9.10-15.el9.x86_64
libutempter-1.2.1-6.el9.x86_64
libuuid-2.37.4-21.el9.x86_64
libverto-0.3.2-3.el9.x86_64
libxcrypt-4.4.18-3.el9.x86_64
libxml2-2.9.13-14.el9_7.x86_64
libzstd-1.5.5-1.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-6.2-12.20210508.el9.x86_64
ncurses-base-6.2-12.20210508.el9.noarch
ncurses-libs-6.2-12.20210508.el9.x86_64
ocaml-srpm-macros-6-6.el9.noarch
openblas-srpm-macros-2-11.el9.noarch
openldap-2.6.8-4.el9.x86_64
openssl-3.5.1-5.el9_7.x86_64
openssl-fips-provider-3.0.7-8.el9.x86_64
openssl-fips-provider-so-3.0.7-8.el9.x86_64
openssl-libs-3.5.1-5.el9_7.x86_64
p11-kit-0.25.3-3.el9_5.x86_64
p11-kit-trust-0.25.3-3.el9_5.x86_64
pam-1.5.1-26.el9_6.x86_64
patch-2.7.6-16.el9.x86_64
pcre-8.44-4.el9.x86_64
pcre2-10.40-6.el9.x86_64
pcre2-syntax-10.40-6.el9.noarch
perl-AutoLoader-5.74-481.1.el9_6.noarch
perl-B-1.80-481.1.el9_6.x86_64
perl-Carp-1.50-460.el9.noarch
perl-Class-Struct-0.66-481.1.el9_6.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-1.30-481.1.el9_6.x86_64
perl-Exporter-5.74-461.el9.noarch
perl-Fcntl-1.13-481.1.el9_6.x86_64
perl-File-Basename-2.85-481.1.el9_6.noarch
perl-File-Path-2.18-4.el9.noarch
perl-File-Temp-0.231.100-4.el9.noarch
perl-File-stat-1.09-481.1.el9_6.noarch
perl-FileHandle-2.03-481.1.el9_6.noarch
perl-Getopt-Long-2.52-4.el9.noarch
perl-Getopt-Std-1.12-481.1.el9_6.noarch
perl-HTTP-Tiny-0.076-462.el9.noarch
perl-IO-1.43-481.1.el9_6.x86_64
perl-IO-Socket-IP-0.41-5.el9.noarch
perl-IO-Socket-SSL-2.073-2.el9.noarch
perl-IPC-Open3-1.21-481.1.el9_6.noarch
perl-MIME-Base64-3.16-4.el9.x86_64
perl-Mozilla-CA-20200520-6.el9.noarch
perl-Net-SSLeay-1.94-3.el9.x86_64
perl-POSIX-1.94-481.1.el9_6.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-1.56-462.el9.x86_64
perl-SelectSaver-1.02-481.1.el9_6.noarch
perl-Socket-2.031-4.el9.x86_64
perl-Storable-3.21-460.el9.x86_64
perl-Symbol-1.08-481.1.el9_6.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-2.27-481.1.el9_6.noarch
perl-constant-1.33-461.el9.noarch
perl-if-0.60.800-481.1.el9_6.noarch
perl-interpreter-5.32.1-481.1.el9_6.x86_64
perl-libnet-3.13-4.el9.noarch
perl-libs-5.32.1-481.1.el9_6.x86_64
perl-mro-1.23-481.1.el9_6.x86_64
perl-overload-1.31-481.1.el9_6.noarch
perl-overloading-0.02-481.1.el9_6.noarch
perl-parent-0.238-460.el9.noarch
perl-podlators-4.14-460.el9.noarch
perl-srpm-macros-1-41.el9.noarch
perl-subs-1.03-481.1.el9_6.noarch
perl-vars-1.05-481.1.el9_6.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-1.16.2-1.el9.noarch
python-srpm-macros-3.9-54.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-9.7-0.7.el9.x86_64
redhat-rpm-config-210-1.el9.noarch
rpm-4.16.1.3-39.el9.x86_64
rpm-build-4.16.1.3-39.el9.x86_64
rpm-build-libs-4.16.1.3-39.el9.x86_64
rpm-libs-4.16.1.3-39.el9.x86_64
rpmautospec-rpm-macros-0.8.1-11.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-4.9-15.el9.x86_64
sqlite-libs-3.34.1-9.el9_7.x86_64
systemd-libs-252-55.el9_7.7.x86_64
tar-1.34-9.el9_7.x86_64
tzdata-2025c-1.el9.noarch
unzip-6.0-59.el9.x86_64
util-linux-2.37.4-21.el9.x86_64
util-linux-core-2.37.4-21.el9.x86_64
which-2.21-30.el9_6.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-1.5.5-1.el9.x86_64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/samtools-1.23-1.el9.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/rhel+epel-9-x86_64-1769509256.406503/root/var/log/dnf.rpm.log
/var/lib/mock/rhel+epel-9-x86_64-1769509256.406503/root/var/log/dnf.librepo.log
/var/lib/mock/rhel+epel-9-x86_64-1769509256.406503/root/var/log/dnf.log
INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz
/bin/tar: Removing leading `/' from member names
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-i8epto6n/samtools/samtools.spec) Config(child) 0 minutes 13 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/samtools-1.23-1.el9.src.rpm)  Config(rhel+epel-9-x86_64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-x86_64-bootstrap-1769509256.406503/root.
INFO: reusing tmpfs at /var/lib/mock/rhel+epel-9-x86_64-bootstrap-1769509256.406503/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-x86_64-1769509256.406503/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.16.1.3-39.el9.x86_64
  python3-dnf-4.14.0-31.el9.noarch
  python3-dnf-plugins-core-4.3.0-24.el9_7.noarch
  yum-4.14.0-31.el9.noarch
Finish: chroot init
Start: build phase for samtools-1.23-1.el9.src.rpm
Start: build setup for samtools-1.23-1.el9.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/samtools-1.23-1.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                                  97 kB/s | 1.5 kB     00:00    
Red Hat Enterprise Linux - BaseOS                39 kB/s | 4.1 kB     00:00    
Red Hat Enterprise Linux - AppStream             57 kB/s | 4.5 kB     00:00    
Red Hat Enterprise Linux - CodeReady Linux Buil  49 kB/s | 4.5 kB     00:00    
Extra Packages for Enterprise Linux 9 - x86_64   85 kB/s |  23 kB     00:00    
Package perl-Getopt-Long-1:2.52-4.el9.noarch is already installed.
Package perl-interpreter-4:5.32.1-481.1.el9_6.x86_64 is already installed.
Dependencies resolved.
================================================================================
 Package               Arch      Version                     Repository    Size
================================================================================
Installing:
 gcc                   x86_64    11.5.0-11.el9               appstream     32 M
 htslib-devel          x86_64    1.23-1.el9                  copr_base    107 k
 htslib-tools          x86_64    1.23-1.el9                  copr_base    730 k
 make                  x86_64    1:4.3-8.el9                 baseos       541 k
 ncurses-devel         x86_64    6.2-12.20210508.el9         appstream    728 k
 perl-FindBin          noarch    1.51-481.1.el9_6            appstream     14 k
 perl-lib              x86_64    0.65-481.1.el9_6            appstream     14 k
 zlib-devel            x86_64    1.2.11-40.el9               appstream     47 k
Installing dependencies:
 annobin               x86_64    12.98-1.el9                 appstream    1.1 M
 cpp                   x86_64    11.5.0-11.el9               appstream     11 M
 gcc-plugin-annobin    x86_64    11.5.0-11.el9               appstream     37 k
 glibc-devel           x86_64    2.34-231.el9_7.2            appstream     37 k
 glibc-headers         x86_64    2.34-231.el9_7.2            appstream    545 k
 htslib                x86_64    1.23-1.el9                  copr_base    570 k
 kernel-headers        x86_64    5.14.0-611.26.1.el9_7       appstream    2.9 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-filesystem       x86_64    20.1.8-3.el9                appstream    9.2 k
 llvm-libs             x86_64    20.1.8-3.el9                appstream     30 M
 ncurses-c++-libs      x86_64    6.2-12.20210508.el9         appstream     37 k

Transaction Summary
================================================================================
Install  21 Packages

Total size: 81 M
Total download size: 765 k
Installed size: 256 M
Downloading Packages:
[SKIPPED] htslib-1.23-1.el9.x86_64.rpm: Already downloaded                     
[SKIPPED] htslib-devel-1.23-1.el9.x86_64.rpm: Already downloaded               
[SKIPPED] htslib-tools-1.23-1.el9.x86_64.rpm: Already downloaded               
[SKIPPED] libedit-3.1-38.20210216cvs.el9.x86_64.rpm: Already downloaded        
[SKIPPED] make-4.3-8.el9.x86_64.rpm: Already downloaded                        
[SKIPPED] libmpc-1.2.1-4.el9.x86_64.rpm: Already downloaded                    
[SKIPPED] libxcrypt-devel-4.4.18-3.el9.x86_64.rpm: Already downloaded          
[SKIPPED] zlib-devel-1.2.11-40.el9.x86_64.rpm: Already downloaded              
[SKIPPED] perl-FindBin-1.51-481.1.el9_6.noarch.rpm: Already downloaded         
[SKIPPED] perl-lib-0.65-481.1.el9_6.x86_64.rpm: Already downloaded             
[SKIPPED] annobin-12.98-1.el9.x86_64.rpm: Already downloaded                   
[SKIPPED] cpp-11.5.0-11.el9.x86_64.rpm: Already downloaded                     
[SKIPPED] gcc-11.5.0-11.el9.x86_64.rpm: Already downloaded                     
[SKIPPED] gcc-plugin-annobin-11.5.0-11.el9.x86_64.rpm: Already downloaded      
[SKIPPED] llvm-filesystem-20.1.8-3.el9.x86_64.rpm: Already downloaded          
[SKIPPED] llvm-libs-20.1.8-3.el9.x86_64.rpm: Already downloaded                
[SKIPPED] glibc-devel-2.34-231.el9_7.2.x86_64.rpm: Already downloaded          
[SKIPPED] glibc-headers-2.34-231.el9_7.2.x86_64.rpm: Already downloaded        
[SKIPPED] kernel-headers-5.14.0-611.26.1.el9_7.x86_64.rpm: Already downloaded  
(20/21): ncurses-c++-libs-6.2-12.20210508.el9.x 385 kB/s |  37 kB     00:00    
(21/21): ncurses-devel-6.2-12.20210508.el9.x86_ 3.7 MB/s | 728 kB     00:00    
--------------------------------------------------------------------------------
Total                                           3.8 MB/s | 765 kB     00:00     
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                             1/21 
  Installing       : htslib-1.23-1.el9.x86_64                              2/21 
  Installing       : cpp-11.5.0-11.el9.x86_64                              3/21 
  Installing       : kernel-headers-5.14.0-611.26.1.el9_7.x86_64           4/21 
  Installing       : glibc-headers-2.34-231.el9_7.2.x86_64                 5/21 
  Installing       : glibc-devel-2.34-231.el9_7.2.x86_64                   6/21 
  Installing       : libxcrypt-devel-4.4.18-3.el9.x86_64                   7/21 
  Installing       : llvm-filesystem-20.1.8-3.el9.x86_64                   8/21 
  Installing       : ncurses-c++-libs-6.2-12.20210508.el9.x86_64           9/21 
  Installing       : make-1:4.3-8.el9.x86_64                              10/21 
  Installing       : gcc-11.5.0-11.el9.x86_64                             11/21 
  Running scriptlet: gcc-11.5.0-11.el9.x86_64                             11/21 
  Installing       : libedit-3.1-38.20210216cvs.el9.x86_64                12/21 
  Installing       : llvm-libs-20.1.8-3.el9.x86_64                        13/21 
  Installing       : annobin-12.98-1.el9.x86_64                           14/21 
  Running scriptlet: annobin-12.98-1.el9.x86_64                           14/21 
  Installing       : gcc-plugin-annobin-11.5.0-11.el9.x86_64              15/21 
  Running scriptlet: gcc-plugin-annobin-11.5.0-11.el9.x86_64              15/21 
  Installing       : ncurses-devel-6.2-12.20210508.el9.x86_64             16/21 
  Installing       : htslib-devel-1.23-1.el9.x86_64                       17/21 
  Installing       : htslib-tools-1.23-1.el9.x86_64                       18/21 
  Installing       : perl-lib-0.65-481.1.el9_6.x86_64                     19/21 
  Installing       : perl-FindBin-1.51-481.1.el9_6.noarch                 20/21 
  Installing       : zlib-devel-1.2.11-40.el9.x86_64                      21/21 
  Running scriptlet: zlib-devel-1.2.11-40.el9.x86_64                      21/21 
  Verifying        : htslib-1.23-1.el9.x86_64                              1/21 
  Verifying        : htslib-devel-1.23-1.el9.x86_64                        2/21 
  Verifying        : htslib-tools-1.23-1.el9.x86_64                        3/21 
  Verifying        : libedit-3.1-38.20210216cvs.el9.x86_64                 4/21 
  Verifying        : make-1:4.3-8.el9.x86_64                               5/21 
  Verifying        : libmpc-1.2.1-4.el9.x86_64                             6/21 
  Verifying        : libxcrypt-devel-4.4.18-3.el9.x86_64                   7/21 
  Verifying        : zlib-devel-1.2.11-40.el9.x86_64                       8/21 
  Verifying        : perl-FindBin-1.51-481.1.el9_6.noarch                  9/21 
  Verifying        : perl-lib-0.65-481.1.el9_6.x86_64                     10/21 
  Verifying        : annobin-12.98-1.el9.x86_64                           11/21 
  Verifying        : cpp-11.5.0-11.el9.x86_64                             12/21 
  Verifying        : ncurses-c++-libs-6.2-12.20210508.el9.x86_64          13/21 
  Verifying        : gcc-11.5.0-11.el9.x86_64                             14/21 
  Verifying        : gcc-plugin-annobin-11.5.0-11.el9.x86_64              15/21 
  Verifying        : llvm-filesystem-20.1.8-3.el9.x86_64                  16/21 
  Verifying        : llvm-libs-20.1.8-3.el9.x86_64                        17/21 
  Verifying        : ncurses-devel-6.2-12.20210508.el9.x86_64             18/21 
  Verifying        : glibc-devel-2.34-231.el9_7.2.x86_64                  19/21 
  Verifying        : glibc-headers-2.34-231.el9_7.2.x86_64                20/21 
  Verifying        : kernel-headers-5.14.0-611.26.1.el9_7.x86_64          21/21 
Installed products updated.

Installed:
  annobin-12.98-1.el9.x86_64                                                    
  cpp-11.5.0-11.el9.x86_64                                                      
  gcc-11.5.0-11.el9.x86_64                                                      
  gcc-plugin-annobin-11.5.0-11.el9.x86_64                                       
  glibc-devel-2.34-231.el9_7.2.x86_64                                           
  glibc-headers-2.34-231.el9_7.2.x86_64                                         
  htslib-1.23-1.el9.x86_64                                                      
  htslib-devel-1.23-1.el9.x86_64                                                
  htslib-tools-1.23-1.el9.x86_64                                                
  kernel-headers-5.14.0-611.26.1.el9_7.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-filesystem-20.1.8-3.el9.x86_64                                           
  llvm-libs-20.1.8-3.el9.x86_64                                                 
  make-1:4.3-8.el9.x86_64                                                       
  ncurses-c++-libs-6.2-12.20210508.el9.x86_64                                   
  ncurses-devel-6.2-12.20210508.el9.x86_64                                      
  perl-FindBin-1.51-481.1.el9_6.noarch                                          
  perl-lib-0.65-481.1.el9_6.x86_64                                              
  zlib-devel-1.2.11-40.el9.x86_64                                               

Complete!
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/samtools-1.23-1.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                                  40 kB/s | 1.5 kB     00:00    
Red Hat Enterprise Linux - BaseOS                41 kB/s | 4.1 kB     00:00    
Red Hat Enterprise Linux - AppStream             54 kB/s | 4.5 kB     00:00    
Red Hat Enterprise Linux - CodeReady Linux Buil  42 kB/s | 4.5 kB     00:00    
Extra Packages for Enterprise Linux 9 - x86_64   92 kB/s |  23 kB     00:00    
Package gcc-11.5.0-11.el9.x86_64 is already installed.
Package htslib-devel-1.23-1.el9.x86_64 is already installed.
Package htslib-tools-1.23-1.el9.x86_64 is already installed.
Package make-1:4.3-8.el9.x86_64 is already installed.
Package ncurses-devel-6.2-12.20210508.el9.x86_64 is already installed.
Package perl-FindBin-1.51-481.1.el9_6.noarch is already installed.
Package perl-Getopt-Long-1:2.52-4.el9.noarch is already installed.
Package perl-lib-0.65-481.1.el9_6.x86_64 is already installed.
Package perl-interpreter-4:5.32.1-481.1.el9_6.x86_64 is already installed.
Package zlib-devel-1.2.11-40.el9.x86_64 is already installed.
Dependencies resolved.
Nothing to do.
Complete!
Finish: build setup for samtools-1.23-1.el9.src.rpm
Start: rpmbuild samtools-1.23-1.el9.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1769040000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.ryFtPz
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf samtools-1.23
+ /usr/bin/bzip2 -dc /builddir/build/SOURCES/samtools-1.23.tar.bz2
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd samtools-1.23
+ /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.suF4Ct
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.23
+ 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' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./htslib-1.23/config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./htslib-1.23/config.guess
++ basename ./htslib-1.23/config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./htslib-1.23/config.guess
'/usr/lib/rpm/redhat/config.guess' -> './htslib-1.23/config.guess'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./htslib-1.23/config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./htslib-1.23/config.sub
++ basename ./htslib-1.23/config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./htslib-1.23/config.sub
'/usr/lib/rpm/redhat/config.sub' -> './htslib-1.23/config.sub'
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ 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 -j4 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_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_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 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_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 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_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_color.o bam_color.c
echo '#define SAMTOOLS_VERSION "1.23"' > version.h
echo '#define SAMTOOLS_CC "gcc"' >> version.h
echo '#define SAMTOOLS_CPPFLAGS ""' >> version.h
echo '#define SAMTOOLS_CFLAGS "-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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 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 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 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 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 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 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 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 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 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 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 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 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 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_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 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 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_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 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_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_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_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 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 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 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 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 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 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 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 bam_checksum.o bam_checksum.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 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 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/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 -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 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 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 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
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
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_bam_translate.o test/merge/test_bam_translate.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/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 misc/md5fa misc/md5fa.o -lhts -lz 
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  -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 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 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/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/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/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/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 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/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 samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o bam_checksum.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz  -lpthread
lto-wrapper: warning: using serial compilation of 11 LTRANS jobs
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.QhkyVX
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64
++ dirname /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64
+ cd samtools-1.23
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/share/man/man1
/usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.23-1.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-1.23-1.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-1.23-1.el9.x86_64/usr/bin
/usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/share/man/man1
++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/zoom2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/blast2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/bowtie2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/export2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/fasta-sanitize.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/interpolate_sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/novo2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/plot-ampliconstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/plot-bamstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/psl2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/sam2vcf.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/samtools.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/seq_cache_populate.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/soap2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/wgsim_eval.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/zoom2sam.pl
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.23-1.el9 --unique-debug-suffix -1.23-1.el9.x86_64 --unique-debug-src-base samtools-1.23-1.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-1.23
extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/ace2sam
extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/maq2sam-long
extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/maq2sam-short
extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/md5fa
extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/samtools
extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/wgsim
extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/bin/md5sum-lite
original debug info size: 2440kB, size after compression: 2196kB
/usr/bin/sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match.
3173 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.emBTg9
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.23
+ ldd samtools
+ grep -E -e '/lib(64)?/libhts\.so\.' -e '/lib64/lp64d/libhts\.so\.'
	libhts.so.3 => /lib64/libhts.so.3 (0x00007fde071fb000)
+ make test
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
test/split/test_parse_args
REF_PATH=: test/test.pl --exec bgzip= ${TEST_OPTS:-}
test_reference:
	/builddir/build/BUILD/samtools-1.23/samtools reference test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23/samtools reference -e test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
.. ok

bgzip -c -b 65272 -s 5 /tmp/MmJOJKN25p/bgzip.dat.gz
.. ok

bgzip -c -b 979200 -s 6 /tmp/MmJOJKN25p/bgzip.dat.gz
.. ok

bgzip -c -b 652804 -s 6 /tmp/MmJOJKN25p/bgzip.dat.gz
.. ok

/builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/MmJOJKN25p/faidx.fa 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/MmJOJKN25p/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/MmJOJKN25p/faidx.fa 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/MmJOJKN25p/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/MmJOJKN25p/faidx.fa 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/MmJOJKN25p/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/MmJOJKN25p/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/MmJOJKN25p/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/MmJOJKN25p/fqidx.fq 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/MmJOJKN25p/fqidx.fq.gz 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/MmJOJKN25p/fqidx.fq 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/MmJOJKN25p/fqidx.fq.gz 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/MmJOJKN25p/fqidx.fq 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/MmJOJKN25p/fqidx.fq.gz 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/MmJOJKN25p/fqidx.fq 1:99998-100007
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/MmJOJKN25p/fqidx.fq.gz 1:99998-100007
.. ok

.. ok

test_dict:
	/builddir/build/BUILD/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /builddir/build/BUILD/samtools-1.23/test/dat/dict.fa
.. ok

test_dict:
	/builddir/build/BUILD/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/MmJOJKN25p/dict.fa.gz
.. ok

test_dict:
	cat /builddir/build/BUILD/samtools-1.23/test/dat/dict.fa | /builddir/build/BUILD/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz
.. ok

test_dict:
	/builddir/build/BUILD/samtools-1.23/samtools dict -AH < /builddir/build/BUILD/samtools-1.23/test/dat/dict.alias.fa
.. ok

test_dict:
	/builddir/build/BUILD/samtools-1.23/samtools dict -H -l /builddir/build/BUILD/samtools-1.23/test/dat/dict.alt < /builddir/build/BUILD/samtools-1.23/test/dat/dict.alias.fa
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools view /tmp/MmJOJKN25p/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools view /tmp/MmJOJKN25p/large_chrom.bam ref2:1-541556283
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/MmJOJKN25p/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/MmJOJKN25p/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools merge -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai /tmp/MmJOJKN25p/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/MmJOJKN25p/test_input_1_b_opt.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools index -M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam && cat /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools index -c /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam /tmp/MmJOJKN25p/auto_indexed.csi && cat /tmp/MmJOJKN25p/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.cram /tmp/MmJOJKN25p/auto_indexed.crai && cat /tmp/MmJOJKN25p/auto_indexed.crai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools index -c /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.sam /tmp/MmJOJKN25p/auto_indexed.csi && cat /tmp/MmJOJKN25p/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools view -@ 2 /tmp/MmJOJKN25p/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools view -@ 2 /tmp/MmJOJKN25p/large_chrom.bam ref2:1-541556283
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/MmJOJKN25p/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/MmJOJKN25p/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai /tmp/MmJOJKN25p/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/MmJOJKN25p/test_input_1_b_opt.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools index -@ 2 -M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam && cat /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam /tmp/MmJOJKN25p/auto_indexed.csi && cat /tmp/MmJOJKN25p/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.cram /tmp/MmJOJKN25p/auto_indexed.crai && cat /tmp/MmJOJKN25p/auto_indexed.crai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.sam /tmp/MmJOJKN25p/auto_indexed.csi && cat /tmp/MmJOJKN25p/auto_indexed.csi
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/MmJOJKN25p/mpileup.bam.list -f /tmp/MmJOJKN25p/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/MmJOJKN25p/mpileup.cram.list -f /tmp/MmJOJKN25p/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/MmJOJKN25p/mpileup.bam.urllist -f /tmp/MmJOJKN25p/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/MmJOJKN25p/mpileup.cram.urllist -f /tmp/MmJOJKN25p/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/MmJOJKN25p/mpileup.ref.fa.gz -r17:1050-1060 /tmp/MmJOJKN25p/mpileup.1.bam | grep -v mpileup
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/MmJOJKN25p/mpileup.ref.fa.gz -r17:1050-1060 /tmp/MmJOJKN25p/mpileup.1.cram | grep -v mpileup
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23/samtools mpileup /builddir/build/BUILD/samtools-1.23/test/mpileup/overlap.bam | grep 128814202
test/test.pl: no IO::Pty module or can't open pty; skipping usage tests
.. ok

test_usage:
	samtools
test_view:
	Generating test data file .................. done
	1: SAM -> BAM -> SAM                                        .. ok

	2: SAM -> uncompressed BAM                                  .. ok

	3: uncompressed BAM -> SAM and compare                      .. ok

	4: SAM -> fast compressed BAM                               .. ok

	5: fast compressed BAM -> SAM and compare                   .. ok

	6: SAM -> CRAM -> SAM (UR header tags)                      .. ok

	7: SAM -> CRAM -> SAM (M5 header tags)                      .. ok

	8: BAM -> CRAM with UR -> SAM                               .. ok

	9: SAM -> BAM (M5 header tags)                              .. ok

	10: SAM -> BAM -> CRAM -> SAM (M5 header tags)              .. ok

	11: CRAM -> BAM with UR                                     .. ok

	12: CRAM -> BAM with M5                                     .. ok

	13: SAM -> SAM via stdout                                   .. ok

	14: SAM -> BAM via stdout                                   .. ok

	15: SAM -> CRAM via stdout                                  .. ok

	16: SAM from stdin -> SAM                                   .. ok

	17: BAM from stdin -> SAM                                   .. ok

	18: CRAM from stdin -> SAM                                  .. ok

	19: samtools view -H (SAM input)                            .. ok

	20: samtools view -H (BAM input)                            .. ok

	21: samtools view -H (CRAM input)                           .. ok

	22: No headers (SAM input)                                  .. ok

	23: No headers (BAM input)                                  .. ok

	24: No headers (CRAM input)                                 .. ok

	25: Filter -f 128 (SAM input)                               .. ok

	26: Count -f 128 (SAM input)                                .. ok

	27: Filter -f 128 (BAM input)                               .. ok

	28: Count -f 128 (BAM input)                                .. ok

	29: Filter -f 128 (CRAM input)                              .. ok

	30: Count -f 128 (CRAM input)                               .. ok

	31: Filter -F 128 (SAM input)                               .. ok

	32: Count -F 128 (SAM input)                                .. ok

	33: Filter -F 128 (BAM input)                               .. ok

	34: Count -F 128 (BAM input)                                .. ok

	35: Filter -F 128 (CRAM input)                              .. ok

	36: Count -F 128 (CRAM input)                               .. ok

	37: Filter -F 128 -f 2 (SAM input)                          .. ok

	38: Count -F 128 -f 2 (SAM input)                           .. ok

	39: Filter -F 128 -f 2 (BAM input)                          .. ok

	40: Count -F 128 -f 2 (BAM input)                           .. ok

	41: Filter -F 128 -f 2 (CRAM input)                         .. ok

	42: Count -F 128 -f 2 (CRAM input)                          .. ok

	43: Filter -r grp2 (SAM input)                              .. ok

	44: Count -r grp2 (SAM input)                               .. ok

	45: Filter -r grp2 (BAM input)                              .. ok

	46: Count -r grp2 (BAM input)                               .. ok

	47: Filter -r grp2 (CRAM input)                             .. ok

	48: Count -r grp2 (CRAM input)                              .. ok

	49: Filter -R /tmp/MmJOJKN25p/view.001.fogn (SAM input)     .. ok

	50: Count -R /tmp/MmJOJKN25p/view.001.fogn (SAM input)      .. ok

	51: Filter -R /tmp/MmJOJKN25p/view.001.fogn (BAM input)     .. ok

	52: Count -R /tmp/MmJOJKN25p/view.001.fogn (BAM input)      .. ok

	53: Filter -R /tmp/MmJOJKN25p/view.001.fogn (CRAM input)    .. ok

	54: Count -R /tmp/MmJOJKN25p/view.001.fogn (CRAM input)     .. ok

	55: Filter -R /tmp/MmJOJKN25p/view.001.fogn -r grp2 (SAM input).. ok

	56: Count -R /tmp/MmJOJKN25p/view.001.fogn -r grp2 (SAM input).. ok

	57: Filter -R /tmp/MmJOJKN25p/view.001.fogn -r grp2 (BAM input).. ok

	58: Count -R /tmp/MmJOJKN25p/view.001.fogn -r grp2 (BAM input).. ok

	59: Filter -R /tmp/MmJOJKN25p/view.001.fogn -r grp2 (CRAM input).. ok

	60: Count -R /tmp/MmJOJKN25p/view.001.fogn -r grp2 (CRAM input).. ok

	61: Filter -r grp2 -R /tmp/MmJOJKN25p/view.001.fogn (SAM input).. ok

	62: Count -r grp2 -R /tmp/MmJOJKN25p/view.001.fogn (SAM input).. ok

	63: Filter -r grp2 -R /tmp/MmJOJKN25p/view.001.fogn (BAM input).. ok

	64: Count -r grp2 -R /tmp/MmJOJKN25p/view.001.fogn (BAM input).. ok

	65: Filter -r grp2 -R /tmp/MmJOJKN25p/view.001.fogn (CRAM input).. ok

	66: Count -r grp2 -R /tmp/MmJOJKN25p/view.001.fogn (CRAM input).. ok

	67: Filter -N /tmp/MmJOJKN25p/view.001.forn (SAM input)     .. ok

	68: Count -N /tmp/MmJOJKN25p/view.001.forn (SAM input)      .. ok

	69: Filter -N /tmp/MmJOJKN25p/view.001.forn (BAM input)     .. ok

	70: Count -N /tmp/MmJOJKN25p/view.001.forn (BAM input)      .. ok

	71: Filter -N /tmp/MmJOJKN25p/view.001.forn (CRAM input)    .. ok

	72: Count -N /tmp/MmJOJKN25p/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/MmJOJKN25p/view.001.fobc (SAM input)  .. ok

	86: Count -D BC:/tmp/MmJOJKN25p/view.001.fobc (SAM input)   .. ok

	87: Filter -D BC:/tmp/MmJOJKN25p/view.001.fobc (BAM input)  .. ok

	88: Count -D BC:/tmp/MmJOJKN25p/view.001.fobc (BAM input)   .. ok

	89: Filter -D BC:/tmp/MmJOJKN25p/view.001.fobc (CRAM input) .. ok

	90: Count -D BC:/tmp/MmJOJKN25p/view.001.fobc (CRAM input)  .. ok

	91: Filter -D BC:/tmp/MmJOJKN25p/view.001.fobc -d BC:TGCA (SAM input).. ok

	92: Count -D BC:/tmp/MmJOJKN25p/view.001.fobc -d BC:TGCA (SAM input).. ok

	93: Filter -D BC:/tmp/MmJOJKN25p/view.001.fobc -d BC:TGCA (BAM input).. ok

	94: Count -D BC:/tmp/MmJOJKN25p/view.001.fobc -d BC:TGCA (BAM input).. ok

	95: Filter -D BC:/tmp/MmJOJKN25p/view.001.fobc -d BC:TGCA (CRAM input).. ok

	96: Count -D BC:/tmp/MmJOJKN25p/view.001.fobc -d BC:TGCA (CRAM input).. ok

	97: Filter -d BC:TGCA -D BC:/tmp/MmJOJKN25p/view.001.fobc (SAM input).. ok

	98: Count -d BC:TGCA -D BC:/tmp/MmJOJKN25p/view.001.fobc (SAM input).. ok

	99: Filter -d BC:TGCA -D BC:/tmp/MmJOJKN25p/view.001.fobc (BAM input).. ok

	100: Count -d BC:TGCA -D BC:/tmp/MmJOJKN25p/view.001.fobc (BAM input).. ok

	101: Filter -d BC:TGCA -D BC:/tmp/MmJOJKN25p/view.001.fobc (CRAM input).. ok

	102: Count -d BC:TGCA -D BC:/tmp/MmJOJKN25p/view.001.fobc (CRAM input).. ok

	103: Filter -D RG:/tmp/MmJOJKN25p/view.001.fogn (SAM input) .. ok

	104: Count -D RG:/tmp/MmJOJKN25p/view.001.fogn (SAM input)  .. ok

	105: Filter -D RG:/tmp/MmJOJKN25p/view.001.fogn (BAM input) .. ok

	106: Count -D RG:/tmp/MmJOJKN25p/view.001.fogn (BAM input)  .. ok

	107: Filter -D RG:/tmp/MmJOJKN25p/view.001.fogn (CRAM input).. ok

	108: Count -D RG:/tmp/MmJOJKN25p/view.001.fogn (CRAM input) .. ok

	109: Filter -d NE:TGCA (SAM input)                          .. ok

	110: Count -d NE:TGCA (SAM input)                           .. ok

	111: Filter -d NE:TGCA (BAM input)                          .. ok

	112: Count -d NE:TGCA (BAM input)                           .. ok

	113: Filter -d NE:TGCA (CRAM input)                         .. ok

	114: Count -d NE:TGCA (CRAM input)                          .. ok

	115: Filter -d TGCA (SAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/MmJOJKN25p/view.test115.sam -h -d TGCA /tmp/MmJOJKN25p/view.001.sam --no-PG


.. expected failure

	116: Count -d TGCA (SAM input)                              samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -c -d TGCA /tmp/MmJOJKN25p/view.001.sam --no-PG


.. expected failure

	117: Filter -d TGCA (BAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/MmJOJKN25p/view.test117.sam -h -d TGCA /tmp/MmJOJKN25p/view.test001.bam --no-PG


.. expected failure

	118: Count -d TGCA (BAM input)                              samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -c -d TGCA /tmp/MmJOJKN25p/view.test001.bam --no-PG


.. expected failure

	119: Filter -d TGCA (CRAM input)                            samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/MmJOJKN25p/view.test119.sam -h -d TGCA /tmp/MmJOJKN25p/view.test006.cram --no-PG


.. expected failure

	120: Count -d TGCA (CRAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -c -d TGCA /tmp/MmJOJKN25p/view.test006.cram --no-PG


.. expected failure

	121: Filter -D BClong:/tmp/MmJOJKN25p/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/MmJOJKN25p/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/MmJOJKN25p/view.test121.sam -h -D BClong:/tmp/MmJOJKN25p/view.001.fobc /tmp/MmJOJKN25p/view.001.sam --no-PG


.. expected failure

	122: Count -D BClong:/tmp/MmJOJKN25p/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/MmJOJKN25p/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/MmJOJKN25p/view.001.fobc /tmp/MmJOJKN25p/view.001.sam --no-PG


.. expected failure

	123: Filter -D BClong:/tmp/MmJOJKN25p/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/MmJOJKN25p/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/MmJOJKN25p/view.test123.sam -h -D BClong:/tmp/MmJOJKN25p/view.001.fobc /tmp/MmJOJKN25p/view.test001.bam --no-PG


.. expected failure

	124: Count -D BClong:/tmp/MmJOJKN25p/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/MmJOJKN25p/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/MmJOJKN25p/view.001.fobc /tmp/MmJOJKN25p/view.test001.bam --no-PG


.. expected failure

	125: Filter -D BClong:/tmp/MmJOJKN25p/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/MmJOJKN25p/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/MmJOJKN25p/view.test125.sam -h -D BClong:/tmp/MmJOJKN25p/view.001.fobc /tmp/MmJOJKN25p/view.test006.cram --no-PG


.. expected failure

	126: Count -D BClong:/tmp/MmJOJKN25p/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/MmJOJKN25p/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/MmJOJKN25p/view.001.fobc /tmp/MmJOJKN25p/view.test006.cram --no-PG


.. expected failure

	127: Filter -d BC:ACGT -d RG:grp2 (SAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/MmJOJKN25p/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/MmJOJKN25p/view.001.sam --no-PG


.. expected failure

	128: Count -d BC:ACGT -d RG:grp2 (SAM input)                samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/MmJOJKN25p/view.001.sam --no-PG


.. expected failure

	129: Filter -d BC:ACGT -d RG:grp2 (BAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/MmJOJKN25p/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/MmJOJKN25p/view.test001.bam --no-PG


.. expected failure

	130: Count -d BC:ACGT -d RG:grp2 (BAM input)                samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/MmJOJKN25p/view.test001.bam --no-PG


.. expected failure

	131: Filter -d BC:ACGT -d RG:grp2 (CRAM input)              samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/MmJOJKN25p/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/MmJOJKN25p/view.test006.cram --no-PG


.. expected failure

	132: Count -d BC:ACGT -d RG:grp2 (CRAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/MmJOJKN25p/view.test006.cram --no-PG


.. expected failure

	133: Filter -d NM:13 (SAM input)                            .. ok

	134: Count -d NM:13 (SAM input)                             .. ok

	135: Filter -d NM:13 (BAM input)                            .. ok

	136: Count -d NM:13 (BAM input)                             .. ok

	137: Filter -d NM:13 (CRAM input)                           .. ok

	138: Count -d NM:13 (CRAM input)                            .. ok

	139: Filter -d ab:z (SAM input)                             .. ok

	140: Count -d ab:z (SAM input)                              .. ok

	141: Filter -d ab:z (BAM input)                             .. ok

	142: Count -d ab:z (BAM input)                              .. ok

	143: Filter -d ab:z (CRAM input)                            .. ok

	144: Count -d ab:z (CRAM input)                             .. ok

	145: Filter -l Library 2 (SAM input)                        .. ok

	146: Count -l Library 2 (SAM input)                         .. ok

	147: Filter -l Library 2 (BAM input)                        .. ok

	148: Count -l Library 2 (BAM input)                         .. ok

	149: Filter -l Library 2 (CRAM input)                       .. ok

	150: Count -l Library 2 (CRAM input)                        .. ok

	151: Filter -l Library 3 (SAM input)                        .. ok

	152: Count -l Library 3 (SAM input)                         .. ok

	153: Filter -l Library 3 (BAM input)                        .. ok

	154: Count -l Library 3 (BAM input)                         .. ok

	155: Filter -l Library 3 (CRAM input)                       .. ok

	156: Count -l Library 3 (CRAM input)                        .. ok

	157: Filter -q 50 (SAM input)                               .. ok

	158: Count -q 50 (SAM input)                                .. ok

	159: Filter -q 50 (BAM input)                               .. ok

	160: Count -q 50 (BAM input)                                .. ok

	161: Filter -q 50 (CRAM input)                              .. ok

	162: Count -q 50 (CRAM input)                               .. ok

	163: Filter -q 99 (SAM input)                               .. ok

	164: Count -q 99 (SAM input)                                .. ok

	165: Filter -q 99 (BAM input)                               .. ok

	166: Count -q 99 (BAM input)                                .. ok

	167: Filter -q 99 (CRAM input)                              .. ok

	168: Count -q 99 (CRAM input)                               .. ok

	169: Filter -q 100 (SAM input)                              .. ok

	170: Count -q 100 (SAM input)                               .. ok

	171: Filter -q 100 (BAM input)                              .. ok

	172: Count -q 100 (BAM input)                               .. ok

	173: Filter -q 100 (CRAM input)                             .. ok

	174: Count -q 100 (CRAM input)                              .. ok

	175: Filter -x fa (SAM input)                               .. ok

	176: Count -x fa (SAM input)                                .. ok

	177: Filter -x fa (BAM input)                               .. ok

	178: Count -x fa (BAM input)                                .. ok

	179: Filter -x fa (CRAM input)                              .. ok

	180: Count -x fa (CRAM input)                               .. ok

	181: Filter -x fa -x ha (SAM input)                         .. ok

	182: Count -x fa -x ha (SAM input)                          .. ok

	183: Filter -x fa -x ha (BAM input)                         .. ok

	184: Count -x fa -x ha (BAM input)                          .. ok

	185: Filter -x fa -x ha (CRAM input)                        .. ok

	186: Count -x fa -x ha (CRAM input)                         .. ok

	187: Filter -x fa,ha (SAM input)                            .. ok

	188: Count -x fa,ha (SAM input)                             .. ok

	189: Filter -x fa,ha (BAM input)                            .. ok

	190: Count -x fa,ha (BAM input)                             .. ok

	191: Filter -x fa,ha (CRAM input)                           .. ok

	192: Count -x fa,ha (CRAM input)                            .. ok

	193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	205: Filter -x fa -r grp2 (SAM input)                       .. ok

	206: Count -x fa -r grp2 (SAM input)                        .. ok

	207: Filter -x fa -r grp2 (BAM input)                       .. ok

	208: Count -x fa -r grp2 (BAM input)                        .. ok

	209: Filter -x fa -r grp2 (CRAM input)                      .. ok

	210: Count -x fa -r grp2 (CRAM input)                       .. ok

	211: Filter -x RG -r grp2 (SAM input)                       .. ok

	212: Count -x RG -r grp2 (SAM input)                        .. ok

	213: Filter -x RG -r grp2 (BAM input)                       .. ok

	214: Count -x RG -r grp2 (BAM input)                        .. ok

	215: Filter -x RG -r grp2 (CRAM input)                      .. ok

	216: Count -x RG -r grp2 (CRAM input)                       .. ok

	217: Filter -m 10 (SAM input)                               .. ok

	218: Count -m 10 (SAM input)                                .. ok

	219: Filter -m 10 (BAM input)                               .. ok

	220: Count -m 10 (BAM input)                                .. ok

	221: Filter -m 10 (CRAM input)                              .. ok

	222: Count -m 10 (CRAM input)                               .. ok

	223: Filter -m 11 (SAM input)                               .. ok

	224: Count -m 11 (SAM input)                                .. ok

	225: Filter -m 11 (BAM input)                               .. ok

	226: Count -m 11 (BAM input)                                .. ok

	227: Filter -m 11 (CRAM input)                              .. ok

	228: Count -m 11 (CRAM input)                               .. ok

	229: Filter -m 15 (SAM input)                               .. ok

	230: Count -m 15 (SAM input)                                .. ok

	231: Filter -m 15 (BAM input)                               .. ok

	232: Count -m 15 (BAM input)                                .. ok

	233: Filter -m 15 (CRAM input)                              .. ok

	234: Count -m 15 (CRAM input)                               .. ok

	235: Filter -m 16 (SAM input)                               .. ok

	236: Count -m 16 (SAM input)                                .. ok

	237: Filter -m 16 (BAM input)                               .. ok

	238: Count -m 16 (BAM input)                                .. ok

	239: Filter -m 16 (CRAM input)                              .. ok

	240: Count -m 16 (CRAM input)                               .. ok

	241: Filter -e !(flag & 128) && (flag & 2) (SAM input)      .. ok

	242: Count -e !(flag & 128) && (flag & 2) (SAM input)       .. ok

	243: Filter -e !(flag & 128) && (flag & 2) (BAM input)      .. ok

	244: Count -e !(flag & 128) && (flag & 2) (BAM input)       .. ok

	245: Filter -e !(flag & 128) && (flag & 2) (CRAM input)     .. ok

	246: Count -e !(flag & 128) && (flag & 2) (CRAM input)      .. ok

	247: Filter -e [BC] (SAM input)                             .. ok

	248: Count -e [BC] (SAM input)                              .. ok

	249: Filter -e [BC] (BAM input)                             .. ok

	250: Count -e [BC] (BAM input)                              .. ok

	251: Filter -e [BC] (CRAM input)                            .. ok

	252: Count -e [BC] (CRAM input)                             .. ok

	253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok

	254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok

	255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok

	256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok

	257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok

	258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok

	259: Filter -e mapq >= 50 (SAM input)                       .. ok

	260: Count -e mapq >= 50 (SAM input)                        .. ok

	261: Filter -e mapq >= 50 (BAM input)                       .. ok

	262: Count -e mapq >= 50 (BAM input)                        .. ok

	263: Filter -e mapq >= 50 (CRAM input)                      .. ok

	264: Count -e mapq >= 50 (CRAM input)                       .. ok

	265: Filter -e mapq >= 99 (SAM input)                       .. ok

	266: Count -e mapq >= 99 (SAM input)                        .. ok

	267: Filter -e mapq >= 99 (BAM input)                       .. ok

	268: Count -e mapq >= 99 (BAM input)                        .. ok

	269: Filter -e mapq >= 99 (CRAM input)                      .. ok

	270: Count -e mapq >= 99 (CRAM input)                       .. ok

	271: Filter -e mapq >= 100 (SAM input)                      .. ok

	272: Count -e mapq >= 100 (SAM input)                       .. ok

	273: Filter -e mapq >= 100 (BAM input)                      .. ok

	274: Count -e mapq >= 100 (BAM input)                       .. ok

	275: Filter -e mapq >= 100 (CRAM input)                     .. ok

	276: Count -e mapq >= 100 (CRAM input)                      .. ok

	277: 1bp reads file SAM -> BAM -> SAM                       .. ok

	278: 1bp reads file SAM -> CRAM -> SAM                      .. ok

	278: Region  Z (BAM input)                                  .. ok

	279: Count  Z (BAM input)                                   .. ok

	280: Region  Z (CRAM input)                                 .. ok

	281: Count  Z (CRAM input)                                  .. ok

	282: Region  Z:30 (BAM input)                               .. ok

	283: Count  Z:30 (BAM input)                                .. ok

	284: Region  Z:30 (CRAM input)                              .. ok

	285: Count  Z:30 (CRAM input)                               .. ok

	286: Region  Z:20-40 (BAM input)                            .. ok

	287: Count  Z:20-40 (BAM input)                             .. ok

	288: Region  Z:20-40 (CRAM input)                           .. ok

	289: Count  Z:20-40 (CRAM input)                            .. ok

	290: Region  ref1 (BAM input)                               .. ok

	291: Count  ref1 (BAM input)                                .. ok

	292: Region  ref1 (CRAM input)                              .. ok

	293: Count  ref1 (CRAM input)                               .. ok

	294: Region  ref1:15 (BAM input)                            .. ok

	295: Count  ref1:15 (BAM input)                             .. ok

	296: Region  ref1:15 (CRAM input)                           .. ok

	297: Count  ref1:15 (CRAM input)                            .. ok

	298: Region  ref1:15-45 (BAM input)                         .. ok

	299: Count  ref1:15-45 (BAM input)                          .. ok

	300: Region  ref1:15-45 (CRAM input)                        .. ok

	301: Count  ref1:15-45 (CRAM input)                         .. ok

	302: Region  ref1:15-45 ref2 (BAM input)                    .. ok

	303: Count  ref1:15-45 ref2 (BAM input)                     .. ok

	304: Region  ref1:15-45 ref2 (CRAM input)                   .. ok

	305: Count  ref1:15-45 ref2 (CRAM input)                    .. ok

	306: Region  ref1:15-45 ref2:16 (BAM input)                 .. ok

	307: Count  ref1:15-45 ref2:16 (BAM input)                  .. ok

	308: Region  ref1:15-45 ref2:16 (CRAM input)                .. ok

	309: Count  ref1:15-45 ref2:16 (CRAM input)                 .. ok

	310: Region  ref1:15-45 ref2:16-31 (BAM input)              .. ok

	311: Count  ref1:15-45 ref2:16-31 (BAM input)               .. ok

	312: Region  ref1:15-45 ref2:16-31 (CRAM input)             .. ok

	313: Count  ref1:15-45 ref2:16-31 (CRAM input)              .. ok

	314: Region  ref1:15-15 ref1:45-45 (BAM input)              .. ok

	315: Count  ref1:15-15 ref1:45-45 (BAM input)               .. ok

	316: Region  ref1:15-15 ref1:45-45 (CRAM input)             .. ok

	317: Count  ref1:15-15 ref1:45-45 (CRAM input)              .. ok

	318: Region -f 128 ref1 (BAM input)                         .. ok

	319: Count -f 128 ref1 (BAM input)                          .. ok

	320: Region -f 128 ref1 (CRAM input)                        .. ok

	321: Count -f 128 ref1 (CRAM input)                         .. ok

	322: Region -q 50 ref1:15-45 (BAM input)                    .. ok

	323: Count -q 50 ref1:15-45 (BAM input)                     .. ok

	324: Region -q 50 ref1:15-45 (CRAM input)                   .. ok

	325: Count -q 50 ref1:15-45 (CRAM input)                    .. ok

	326: Region -r grp2 ref1:15-45 (BAM input)                  .. ok

	327: Count -r grp2 ref1:15-45 (BAM input)                   .. ok

	328: Region -r grp2 ref1:15-45 (CRAM input)                 .. ok

	329: Count -r grp2 ref1:15-45 (CRAM input)                  .. ok

	330: Region  * (BAM input)                                  .. ok

	331: Count  * (BAM input)                                   .. ok

	332: Region  * (CRAM input)                                 .. ok

	333: Count  * (CRAM input)                                  .. ok

	334: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed  (BAM input).. ok

	335: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed  (BAM input).. ok

	336: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed  (CRAM input).. ok

	337: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed  (CRAM input).. ok

	338: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.02.bed  (BAM input).. ok

	339: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.02.bed  (BAM input).. ok

	340: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.02.bed  (CRAM input).. ok

	341: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.02.bed  (CRAM input).. ok

	342: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed  (BAM input).. ok

	343: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed  (BAM input).. ok

	344: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed  (CRAM input).. ok

	345: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed  (CRAM input).. ok

	346: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.02.bed  (BAM input).. ok

	347: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.02.bed  (BAM input).. ok

	348: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.02.bed  (CRAM input).. ok

	349: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.02.bed  (CRAM input).. ok

	350: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.03.bed  (BAM input).. ok

	351: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.03.bed  (BAM input).. ok

	352: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.03.bed  (CRAM input).. ok

	353: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.03.bed  (CRAM input).. ok

	354: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z (BAM input).. ok

	355: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z (BAM input).. ok

	356: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z (CRAM input).. ok

	357: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z (CRAM input).. ok

	358: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:30 (BAM input).. ok

	359: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:30 (BAM input).. ok

	360: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:30 (CRAM input).. ok

	361: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:30 (CRAM input).. ok

	362: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok

	363: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok

	364: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok

	365: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok

	366: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok

	367: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok

	368: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok

	369: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok

	370: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok

	371: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok

	372: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok

	373: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok

	374: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref2 (BAM input).. ok

	375: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref2 (BAM input).. ok

	376: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref2 (CRAM input).. ok

	377: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref2 (CRAM input).. ok

	378: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok

	379: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok

	380: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok

	381: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok

	382: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1  (BAM input).. ok

	383: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1  (BAM input).. ok

	384: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1  (CRAM input).. ok

	385: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1  (CRAM input).. ok

	386: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -f 128  (BAM input).. ok

	387: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -f 128  (BAM input).. ok

	388: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -f 128  (CRAM input).. ok

	389: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -f 128  (CRAM input).. ok

	390: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -q 5  (BAM input).. ok

	391: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -q 5  (BAM input).. ok

	392: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -q 5  (CRAM input).. ok

	393: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -q 5  (CRAM input).. ok

	394: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok

	395: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok

	396: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok

	397: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok

	398: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap  (BAM input).. ok

	399: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap  (BAM input).. ok

	400: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap  (CRAM input).. ok

	401: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap  (CRAM input).. ok

	402: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok

	403: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok

	404: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok

	405: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok

	406: -L with nested regions                                 .. ok

	407: Make BAM with no M5/UR tags                            .. ok

	408: Add @SQ with -t (SAM -> SAM)                           .. ok

	409: Add @SQ with -T (SAM -> SAM)                           .. ok

	410: Add @SQ with -t (BAM -> SAM)                           .. ok

	411: Add @SQ with -T (BAM -> SAM)                           .. ok

	412: Add @SQ with -t (SAM -> BAM)                           .. ok

	413: Add @SQ with -T (SAM -> BAM)                           .. ok

	414: Add @SQ with -t (BAM -> BAM)                           .. ok

	415: Add @SQ with -T (BAM -> BAM)                           .. ok

	416: Add @SQ with -t (SAM -> CRAM)                          .. ok

	417: Add @SQ with -T (SAM -> CRAM)                          .. ok

	418: Add @SQ with -t (BAM -> CRAM)                          .. ok

	419: Add @SQ with -T (BAM -> CRAM)                          .. ok

	420: Make CRAM with no UR field                             .. ok

	421: Decoding CRAM with no UR field via -T                  .. ok

	422: CIGAR B-operator removal                               .. ok

	423: Big SAM -> BAM                                         .. ok

	424: Big SAM -> BAM (2 threads)                             .. ok

	425: Big SAM -> BAM (4 threads)                             .. ok

	426: Big SAM -> CRAM                                        .. ok

	427: Big SAM -> CRAM (2 threads)                            .. ok

	428: Big SAM -> CRAM (4 threads)                            .. ok

	429: Subsample 0.2 (SAM input) ............ ok

	430: Subsample 0.5 (SAM input) ............ ok

	431: Subsample 0.8 (SAM input) ............ ok

	432: Subsample 0.2 (BAM input) ............ ok

	433: Subsample 0.5 (BAM input) ............ ok

	434: Subsample 0.8 (BAM input) ............ ok

	435: Subsample 0.2 (CRAM input) ............ ok

	436: Subsample 0.5 (CRAM input) ............ ok

	437: Subsample 0.8 (CRAM input) ............ ok

	438: SAM add PG                                             .. ok

	439: Unset dup flag, remove dt and do tags                  .. ok

	440: Unmap dup flagged reads.                               .. ok

	441: Unmap dup flagged reads.                               .. ok

	442: fetch pairs                                            .. ok

	443: fetch pairs                                            .. ok

	444: fetch pairs                                            .. ok

test_head:
	/builddir/build/BUILD/samtools-1.23/samtools head /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23/samtools head -h 0 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23/samtools head -h 1 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23/samtools head -h 5 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23/samtools head -h 29 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23/samtools head -h 30 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23/samtools head -n 0 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23/samtools head -n 1 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23/samtools head -n 5 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23/samtools head -h 5 -n 5 < /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam
.. ok

test_cat:
	Generating test data file .................. done
	Generate BAM file #1                                        .. ok

	Generate BAM region file #1                                 .. ok

	Generate CRAM file #1                                       .. ok

	Generating test data file .................. done
	Generate BAM file #2                                        .. ok

	Generate BAM region file #2                                 .. ok

	Generate CRAM file #2                                       .. ok

	Generating test data file .................. done
	Generate BAM file #3                                        .. ok

	Generate BAM region file #3                                 .. ok

	Generate CRAM file #3                                       .. ok

	Generating test data file .................. done
	Generate BAM file #4                                        .. ok

	Generate BAM region file #4                                 .. ok

	Generate CRAM file #4                                       .. ok

	1: cat BAM files                                            .. ok

	2: cat recompressed BAM files                               .. ok

	3: cat CRAM files                                           .. ok

	4: cat CRAM subregion files                                 .. ok

	5: cat BAM files to stdout                                  .. ok

	6: cat recompressed BAM files to stdout                     .. ok

	7: cat CRAM files to stdout                                 .. ok

	8: cat CRAM subregion files to stdout                       .. ok

	9: cat CRAM part 1/2                                        .. ok

	9: cat CRAM part 2/2                                        .. ok

	9: cat CRAM parts 1/2 + 2/2                                 .. ok

	10: cat BAM files with new header                           .. ok

	11: cat recompressed BAM files with new header              .. ok

	12: cat CRAM files with new header                          .. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected  | /builddir/build/BUILD/samtools-1.23/samtools fastq -0 /builddir/build/BUILD/samtools-1.23/test/0.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG -s test/bam2fq/1.1.fq.expected  | /builddir/build/BUILD/samtools-1.23/samtools fastq -0 /builddir/build/BUILD/samtools-1.23/test/0.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG -s test/bam2fq/5.s.fq.expected  | /builddir/build/BUILD/samtools-1.23/samtools fastq -s /builddir/build/BUILD/samtools-1.23/test/s.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T RG,BC,QT -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T RG,BC,QT,MD,ia -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG	ID:rgid'
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/2.interleaved.fq -T ""
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/3.interleaved.fq -i
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/4.aux.fq -T "*"
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/4.aux.fq -T ""
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG --i1 test/import/5-i1.fq --i2  test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG --i1 test/import/5-i1.fq --i2  test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG -U test/bam2fq/UMI.fq.expected
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23/samtools import --no-PG -U --UMI-tag OX test/bam2fq/UMI.fq.expected
.. ok

test_bam2fq:
	Generate BAM file                                           .. ok

	Generate CRAM file                                          .. ok

	1: fastq  (SAM input)                                       [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	2: fastq -n (SAM input)                                     [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	3: fastq  (BAM input)                                       [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	4: fastq -n (BAM input)                                     [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	5: fastq  (CRAM input)                                      [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	6: fastq -n (CRAM input)                                    [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.002.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.003.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.010.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.23/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -N -t -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.703.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -N -1 /builddir/build/BUILD/samtools-1.23/test/o.fq -2 /builddir/build/BUILD/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fasta  -N -1 /builddir/build/BUILD/samtools-1.23/test/o.fa -2 /builddir/build/BUILD/samtools-1.23/test/o.fa /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -N -o /builddir/build/BUILD/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -N -s /tmp/MmJOJKN25p/bam2fq.discard.s.fq -0 /tmp/MmJOJKN25p/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.013.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.23/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.23/test/i2.fq -0 /builddir/build/BUILD/samtools-1.23/test/0.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.014.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -N -T '' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -N -t -T '*' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -N -T '*' -d MD:10 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -N -T '*' -d NM:0 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -N -T '*' -d ia /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -d NM:13 -d NM:14 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -D NM:test/dat/bam2fq.NM-D /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -D MD:test/dat/bam2fq.MD-D /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -O --no-sc --no-sc-bkp -T 's0' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -O --no-sc -T's0' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -O --no-sc /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq  -O --no-sc --sc-aux s1 -T's0,s1' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -U test/import/UMI.expected.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -U --UMI-tag RX,OX test/import/UMI-OX.expected.sam
.. ok

test_bam2fq:
	Generate BAM file (2 threads)                               .. ok

	Generate CRAM file (2 threads)                              .. ok

	1: fastq  (SAM input) (2 threads)                           [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	2: fastq -n (SAM input) (2 threads)                         [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	3: fastq  (BAM input) (2 threads)                           [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	4: fastq -n (BAM input) (2 threads)                         [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	5: fastq  (CRAM input) (2 threads)                          [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	6: fastq -n (CRAM input) (2 threads)                        [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.002.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.003.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.010.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.23/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -t -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.703.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -1 /builddir/build/BUILD/samtools-1.23/test/o.fq -2 /builddir/build/BUILD/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fasta -@ 2 -N -1 /builddir/build/BUILD/samtools-1.23/test/o.fa -2 /builddir/build/BUILD/samtools-1.23/test/o.fa /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -o /builddir/build/BUILD/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -s /tmp/MmJOJKN25p/bam2fq.discard.s.fq -0 /tmp/MmJOJKN25p/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.013.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.23/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.23/test/i2.fq -0 /builddir/build/BUILD/samtools-1.23/test/0.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.014.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -T '' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -t -T '*' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -T '*' -d MD:10 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -T '*' -d NM:0 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -T '*' -d ia /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -d NM:13 -d NM:14 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -O --no-sc --no-sc-bkp -T 's0' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -O --no-sc -T's0' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -O --no-sc /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -O --no-sc --sc-aux s1 -T's0,s1' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -U test/import/UMI.expected.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23/samtools fastq -U --UMI-tag RX,OX test/import/UMI-OX.expected.sam
.. ok

test_depad:
	Generate BAM file                                           .. ok

	depad  (SAM input)                                          .. ok

	depad -s (SAM input)                                        .. ok

	depad -u (SAM input)                                        .. ok

	depad -1 (SAM input)                                        .. ok

	depad  (BAM input)                                          .. ok

	depad -s (BAM input)                                        .. ok

	depad -u (BAM input)                                        .. ok

	depad -1 (BAM input)                                        .. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/1_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/1_map_cigar_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/4_X_cigar_full_seq.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/5_insert_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/5_insert_cigar_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa -i 0 /builddir/build/BUILD/samtools-1.23/test/stat/5_insert_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/7_supp.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/7_supp_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/8_secondary.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/8_secondary_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/1_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/10_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -t /builddir/build/BUILD/samtools-1.23/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -g 4 -t /builddir/build/BUILD/samtools-1.23/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -g 4 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.23/test/stat/12_3reads.bed | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.23/test/stat/12_3reads.bed | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.23/test/stat/12_2reads.bed | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.23/test/stat/12_2reads.bed | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_ok.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4

	/builddir/build/BUILD/samtools-1.23/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4

	/builddir/build/BUILD/samtools-1.23/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4

	/builddir/build/BUILD/samtools-1.23/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -I s1 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -I grp2 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -I grp3 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -I Sample /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/mpileup/ce.fa /builddir/build/BUILD/samtools-1.23/test/stat/15.big_del.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam | grep -e"^RFS"
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa

	ERR: [E::faidx_adjust_position] The sequence "ref1" was not found
Failed to fetch the sequence "ref1"

.. expected failure

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa | grep -e"^RFS"
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats --ref-stats-chunk -1 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa | grep -e"^RFS"
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa alpha:10-20 | grep -e"^RFS"
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa -t /builddir/build/BUILD/samtools-1.23/test/stat/11.stats.targets  | grep -e"^RFS"
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa -t /builddir/build/BUILD/samtools-1.23/test/stat/11.stats.targets ref1 | grep -e"^RFS"
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam -b /tmp/xW8HGc4N_8 - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b_regex.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/MmJOJKN25p/merge.tag.1.bam /tmp/MmJOJKN25p/merge.tag.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/MmJOJKN25p/merge.tag.3.bam /tmp/MmJOJKN25p/merge.tag.4.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge --no-PG -O SAM - /builddir/build/BUILD/samtools-1.23/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.23/test/merge/merge.bed - /tmp/MmJOJKN25p/merge.bed.1.bam /tmp/MmJOJKN25p/merge.bed.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge --no-PG -r -O SAM - /builddir/build/BUILD/samtools-1.23/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge --no-PG -O SAM --template-coordinate - /builddir/build/BUILD/samtools-1.23/test/merge/test_template_coordinate.1.sam /builddir/build/BUILD/samtools-1.23/test/merge/test_template_coordinate.2.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam -b /tmp/HGEHhjNZ6n - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b_regex.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/MmJOJKN25p/merge.tag.1.bam /tmp/MmJOJKN25p/merge.tag.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/MmJOJKN25p/merge.tag.3.bam /tmp/MmJOJKN25p/merge.tag.4.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM - /builddir/build/BUILD/samtools-1.23/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.23/test/merge/merge.bed - /tmp/MmJOJKN25p/merge.bed.1.bam /tmp/MmJOJKN25p/merge.bed.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 --no-PG -r -O SAM - /builddir/build/BUILD/samtools-1.23/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /builddir/build/BUILD/samtools-1.23/test/merge/test_template_coordinate.1.sam /builddir/build/BUILD/samtools-1.23/test/merge/test_template_coordinate.2.sam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/MmJOJKN25p/sortout
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -f /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/MmJOJKN25p/sortout.bam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -o /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/MmJOJKN25p/sorttmp
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -N -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/sort_name_input_1.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -t RG -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -n -t RG -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -t AS -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -t FI -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort --template-coordinate -m 10M /builddir/build/BUILD/samtools-1.23/test/sort/template-coordinate.sort.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -m 10M -M -K10 -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -m 10M -M -K10 -I /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -m 10M -MH -K10 -I /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/MmJOJKN25p/sortout
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/MmJOJKN25p/sortout.bam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/MmJOJKN25p/sorttmp
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -N -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/sort_name_input_1.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -t RG -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -n -t RG -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -t AS -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -t FI -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 --template-coordinate -m 10M /builddir/build/BUILD/samtools-1.23/test/sort/template-coordinate.sort.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -m 10M -M -K10 -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -m 10M -M -K10 -I /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -m 10M -MH -K10 -I /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23/samtools collate --output-fmt=sam -O /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23/samtools collate -o /builddir/build/BUILD/samtools-1.23/test/collate/collate1.tmp.sam  /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23/samtools collate -o /builddir/build/BUILD/samtools-1.23/test/collate/collate2.tmp.sam  /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23/test/collate/collate2.tmp
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23/samtools collate --output-fmt=sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23/test/collate/collate3.tmp
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23/samtools collate --output-fmt=sam -f /builddir/build/BUILD/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23/test/collate/1_fast_collate.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23/samtools collate --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23/test/collate/2_fast_collate_with_tmp.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 --output-fmt=sam -O /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.23/test/collate/collate1.tmp.sam  /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.23/test/collate/collate2.tmp.sam  /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23/test/collate/collate2.tmp
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 --output-fmt=sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23/test/collate/collate3.tmp
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 --output-fmt=sam -f /builddir/build/BUILD/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23/test/collate/1_fast_collate.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23/test/collate/2_fast_collate_with_tmp.sam
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/1_coord_sort.sam -

	ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.

.. expected failure

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/2_isize_overflow.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.23/test/fixmate/5_ct.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.23/test/fixmate/6_ct_replace.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/7_two_read_mapped.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/8_isize_overflow_64bit.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/sanitize.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ok+.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ok-.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_draft.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated_noML.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated_noMN.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_bad_MN.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_MN_only.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ML_only.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ML_wrong_len.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_noseq.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_bounds.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/1_coord_sort.sam -

	ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.

.. expected failure

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/2_isize_overflow.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.23/test/fixmate/5_ct.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.23/test/fixmate/6_ct_replace.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/7_two_read_mapped.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/8_isize_overflow_64bit.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/sanitize.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ok+.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ok-.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_draft.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated_noML.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated_noMN.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_bad_MN.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_MN_only.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ML_only.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ML_wrong_len.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_noseq.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_bounds.sam -
.. ok

/builddir/build/BUILD/samtools-1.23/samtools calmd -uAr /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa
.. ok

/builddir/build/BUILD/samtools-1.23/samtools calmd -@ 2 -uAr /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa
.. ok

test_idxstat:
	/builddir/build/BUILD/samtools-1.23/samtools idxstats /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam
.. ok

test_idxstat:
	/builddir/build/BUILD/samtools-1.23/samtools idxstats /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.cram
.. ok

test_idxstat:
	/builddir/build/BUILD/samtools-1.23/samtools idxstats /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/1.quickcheck.badeof.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/2.quickcheck.badheader.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/3.quickcheck.ok.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/4.quickcheck.ok.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/5.quickcheck.scramble30.truncated.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/6.quickcheck.cram21.ok.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/7.quickcheck.cram30.ok.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/8.quickcheck.cram21.truncated.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/9.quickcheck.cram30.truncated.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/10.quickcheck.notargets.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23/samtools quickcheck -v  /builddir/build/BUILD/samtools-1.23/test/quickcheck/1.quickcheck.badeof.bam /builddir/build/BUILD/samtools-1.23/test/quickcheck/2.quickcheck.badheader.bam /builddir/build/BUILD/samtools-1.23/test/quickcheck/3.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.23/test/quickcheck/4.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.23/test/quickcheck/5.quickcheck.scramble30.truncated.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/6.quickcheck.cram21.ok.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/7.quickcheck.cram30.ok.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/8.quickcheck.cram21.truncated.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/9.quickcheck.cram30.truncated.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23/samtools quickcheck -uv /builddir/build/BUILD/samtools-1.23/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23/samtools reheader /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23/samtools reheader /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v21.cram | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23/samtools reheader /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23/samtools reheader --in-place /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v21.cram && /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v21.cram | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23/samtools reheader --in-place /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v30.cram && /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v30.cram | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -m orphan_only /builddir/build/BUILD/samtools-1.23/test/addrprg/2_fixup_orphan.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -R '1#9' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.23/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.23/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -m orphan_only /builddir/build/BUILD/samtools-1.23/test/addrprg/2_fixup_orphan.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -R '1#9' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.23/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.23/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/1_name_sort.sam -

	ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/2_bad_order.sam -

	ERR: samtools markdup: error, not in coordinate sorted order.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/3_missing_mc.sam -

	ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first.

samtools markdup: error, unable to assign pair hash key.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/4_missing_ms.sam -

	ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.

samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/5_markdup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -O sam -r --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/6_remove_dups.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -S -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/7_mark_supp_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.23/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.23/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/12_optical_chain_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/13_optical_barcode_tag.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/14_optical_barcode_name.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/15_optical_barcode_rgx_name.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/17_read_group.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /builddir/build/BUILD/samtools-1.23/test/markdup/18_primary_duplicate_count.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/1_name_sort.sam -

	ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/2_bad_order.sam -

	ERR: samtools markdup: error, not in coordinate sorted order.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/3_missing_mc.sam -

	ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first.

samtools markdup: error, unable to assign pair hash key.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/4_missing_ms.sam -

	ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.

samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/5_markdup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam -r --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/6_remove_dups.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/7_mark_supp_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.23/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.23/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/12_optical_chain_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/13_optical_barcode_tag.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/14_optical_barcode_name.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/15_optical_barcode_rgx_name.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/17_read_group.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /builddir/build/BUILD/samtools-1.23/test/markdup/18_primary_duplicate_count.sam -
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.23/samtools bedcov /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.23/samtools bedcov -j /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.23/samtools bedcov -g512 -G2048 /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.23/samtools bedcov -c /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bam
.. ok

.. ok

.. ok

.. ok

.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -p 5 -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  --output-fmt sam -d RG -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  --output-fmt sam -d an -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  --output-fmt sam -d an -M 3 -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.unk.sam  /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam  /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools sort  -t nn /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam |
                /builddir/build/BUILD/samtools-1.23/samtools split  --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam - 
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -p 5 -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  -@ 2 --output-fmt sam -d RG -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  -@ 2 --output-fmt sam -d an -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  -@ 2 --output-fmt sam -d an -M 3 -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.unk.sam  /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools split  -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam  /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23/samtools sort  -@ 2 -t nn /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam |
                /builddir/build/BUILD/samtools-1.23/samtools split  -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam - 
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /tmp/MmJOJKN25p/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /tmp/MmJOJKN25p/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG -L /builddir/build/BUILD/samtools-1.23/test/large_pos/test.bed /tmp/MmJOJKN25p/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23/samtools sort -O sam --no-PG -m 10M /builddir/build/BUILD/samtools-1.23/test/large_pos/longref_name.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23/samtools merge -O sam --no-PG - /builddir/build/BUILD/samtools-1.23/test/large_pos/longref.sam /builddir/build/BUILD/samtools-1.23/test/large_pos/longref2.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23/samtools depth /builddir/build/BUILD/samtools-1.23/test/large_pos/longref.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23/samtools depth -b /builddir/build/BUILD/samtools-1.23/test/large_pos/test.bed /builddir/build/BUILD/samtools-1.23/test/large_pos/longref.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/MmJOJKN25p/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23/samtools sort    -O sam --no-PG -n -m 10M test/large_pos/longref3.sam |
                     /builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam --no-PG - - |
                     /builddir/build/BUILD/samtools-1.23/samtools sort    -O sam --no-PG -m 10M
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG  --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG  --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/2_both_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/3_multi_ref_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test2.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/4_total_hc_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG  --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG  --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/2_both_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/3_multi_ref_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test2.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/4_total_hc_data.sam
.. ok

test_ampliconstats:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_hard_clipped.expected.sam /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_soft_clipped.expected.sam /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_soft_clipped_strand.expected.sam /builddir/build/BUILD/samtools-1.23/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line'
.. ok

test_ampliconstats:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line'
.. ok

test_ampliconstats:
	/builddir/build/BUILD/samtools-1.23/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line'
.. ok

test_reset:
	cat /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag | /builddir/build/BUILD/samtools-1.23/samtools view
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag < /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23/samtools view
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23/samtools view
.. ok

test_reset:
	cat /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.cram
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam -e"@PG	ID:samtools	PN:samtools" | wc -l | sed 's/ //g'
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag --reject-PG sam_to_fixed_bam /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam -e"@PG	ID:" | wc -l | sed 's/ //g'
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index --no-PG /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam -e"@PG"
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG -o /builddir/build/BUILD/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /builddir/build/BUILD/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /builddir/build/BUILD/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /builddir/build/BUILD/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /builddir/build/BUILD/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /builddir/build/BUILD/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /builddir/build/BUILD/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23/test/reset/seq.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23/samtools reset /builddir/build/BUILD/samtools-1.23/test/reset/seq.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum /builddir/build/BUILD/samtools-1.23/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum -a /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum -qv /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum -qv -a /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum -m /builddir/build/BUILD/samtools-1.23/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum -m /builddir/build/BUILD/samtools-1.23/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 /builddir/build/BUILD/samtools-1.23/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -a /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -qv /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -qv -a /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -m /builddir/build/BUILD/samtools-1.23/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -m /builddir/build/BUILD/samtools-1.23/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23/samtools coverage /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 1 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 2 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 2 -Q 8 -q 45 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 1 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam /tmp/MmJOJKN25p/sample1.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 4 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam /tmp/MmJOJKN25p/sample1.sam
.. ok


Number of tests:
    total            .. 998
    passed           .. 966
    failed           .. 0
    expected failure .. 32
    unexpected pass  .. 0

test/merge/test_bam_translate test/merge/test_bam_translate.tmp
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
cd test/mpileup && AWK="gawk" ../regression.sh mpileup.reg

=== Testing mpileup.reg regressions ===
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"

EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam

Expected   passes:   120
Unexpected passes:   0
Expected   failures: 1
Unexpected failures: 0
=> PASS
cd test/mpileup && AWK="gawk" ../regression.sh depth.reg

=== Testing depth.reg regressions ===

EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools depth -a -b xx.bed3 xx#depth3.bam

Expected   passes:   55
Unexpected passes:   0
Expected   failures: 1
Unexpected failures: 0
=> PASS
cd test/mpileup && AWK="gawk" ../regression.sh cram-size.reg

=== Testing cram-size.reg regressions ===

Expected   passes:   5
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
cd test/consensus && AWK="gawk" ../regression.sh consensus.reg

=== Testing consensus.reg regressions ===

Expected   passes:   77
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
cd test/consensus && AWK="gawk" PARAM="-@4 -Z4" ../regression.sh consensus.reg

=== Testing consensus.reg regressions ===

Expected   passes:   77
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
cd test/cram_size && AWK="gawk" ../regression.sh cram_size.reg

=== Testing cram_size.reg regressions ===

Expected   passes:   3
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: samtools-1.23-1.el9.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.pUz94F
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.23
+ DOCDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/share/doc/samtools
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/share/doc/samtools
+ cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/share/doc/samtools
+ cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/share/doc/samtools
+ cp -pr NEWS.md /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/share/doc/samtools
+ cp -pr examples/ /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/share/doc/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.RXcOcz
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.23
+ LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/share/licenses/samtools
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/share/licenses/samtools
+ cp -pr LICENSE /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64/usr/share/licenses/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: samtools = 1.23-1.el9 samtools(x86-64) = 1.23-1.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_1.18)(64bit) libhts.so.3(HTSLIB_1.2.1)(64bit) libhts.so.3(HTSLIB_1.21)(64bit) libhts.so.3(HTSLIB_1.22)(64bit) libhts.so.3(HTSLIB_1.23)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) libhts.so.3(HTSLIB_1.9)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: samtools-debugsource-1.23-1.el9.x86_64
Provides: samtools-debugsource = 1.23-1.el9 samtools-debugsource(x86-64) = 1.23-1.el9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: samtools-debuginfo-1.23-1.el9.x86_64
Provides: debuginfo(build-id) = 80aa46df84235ad4385ba1b98a00f28ed0aaac60 debuginfo(build-id) = 988475c3637b852f505b3f1cd89d661908481b23 debuginfo(build-id) = 9a2c46a6aa1187a389f84a8570dc25b2baa49057 debuginfo(build-id) = bd2382a7cf8ded27c580624ad8ac5927e43349e6 debuginfo(build-id) = d2143e89c9dd6dac36e3d7849dfc0f8c0cbf43d5 debuginfo(build-id) = d9b2428a81ef36ecd8c86ce0fd37d3dd7d7e62eb debuginfo(build-id) = f7498a93032c7327815e57ee586605d0bdc1b23a samtools-debuginfo = 1.23-1.el9 samtools-debuginfo(x86-64) = 1.23-1.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) = 1.23-1.el9
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64
Wrote: /builddir/build/RPMS/samtools-1.23-1.el9.x86_64.rpm
Wrote: /builddir/build/RPMS/samtools-debuginfo-1.23-1.el9.x86_64.rpm
Wrote: /builddir/build/RPMS/samtools-debugsource-1.23-1.el9.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.6BobwL
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.23
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.23-1.el9.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild samtools-1.23-1.el9.src.rpm
Finish: build phase for samtools-1.23-1.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_64-1769509256.406503/root/var/log/dnf.rpm.log
/var/lib/mock/rhel+epel-9-x86_64-1769509256.406503/root/var/log/dnf.librepo.log
/var/lib/mock/rhel+epel-9-x86_64-1769509256.406503/root/var/log/dnf.log
INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz
/bin/tar: Removing leading `/' from member names
INFO: Done(/var/lib/copr-rpmbuild/results/samtools-1.23-1.el9.src.rpm) Config(child) 0 minutes 59 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "samtools-debuginfo",
            "epoch": null,
            "version": "1.23",
            "release": "1.el9",
            "arch": "x86_64"
        },
        {
            "name": "samtools",
            "epoch": null,
            "version": "1.23",
            "release": "1.el9",
            "arch": "src"
        },
        {
            "name": "samtools-debugsource",
            "epoch": null,
            "version": "1.23",
            "release": "1.el9",
            "arch": "x86_64"
        },
        {
            "name": "samtools",
            "epoch": null,
            "version": "1.23",
            "release": "1.el9",
            "arch": "x86_64"
        }
    ]
}
RPMResults finished