Warning: Permanently added '2620:52:6:1161:dead:beef:cafe:c194' (ED25519) to the list of known hosts.

You can reproduce this build on your computer by running:

  sudo dnf install copr-rpmbuild
  /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/10066888-fedora-43-ppc64le --chroot fedora-43-ppc64le


Version: 1.6
PID: 2417
Logging PID: 2419
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'build_id': 10066888,
 'buildroot_pkgs': [],
 'chroot': 'fedora-43-ppc64le',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '624052c1792453848c83aeb6f9b9daebd1bdd335',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ron/staging/samtools',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'samtools',
 'package_version': '1.23-1',
 'project_dirname': 'staging',
 'project_name': 'staging',
 'project_owner': 'ron',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ron/staging/fedora-43-ppc64le/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'ron/staging--ron',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'storage': 0,
 'submitter': 'ron',
 'tags': [],
 'task_id': '10066888-fedora-43-ppc64le',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ron/staging/samtools /var/lib/copr-rpmbuild/workspace/workdir-wmtr0gny/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-wmtr0gny/samtools', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-wmtr0gny/samtools'...

Running: git checkout 624052c1792453848c83aeb6f9b9daebd1bdd335 --

cmd: ['git', 'checkout', '624052c1792453848c83aeb6f9b9daebd1bdd335', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-wmtr0gny/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-wmtr0gny/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
tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-wmtr0gny/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-wmtr0gny/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769509389.082718 -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-wmtr0gny/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-wmtr0gny/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769509389.082718 -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-wmtr0gny/samtools/samtools.spec)  Config(fedora-43-ppc64le)
Start: clean chroot
Finish: clean chroot
Mock Version: 6.6
INFO: Mock Version: 6.6
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-43-ppc64le-bootstrap-1769509389.082718/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.fedoraproject.org/fedora:43
INFO: Pulling image: registry.fedoraproject.org/fedora:43
INFO: Tagging container image as mock-bootstrap-d91a7f98-1b23-4442-b000-a6878e36b85a
INFO: Checking that 18e411c14bbe0ba80799508c4d33fe88381b813f4281b9b61881b74a0526d072 image matches host's architecture
INFO: Copy content of container 18e411c14bbe0ba80799508c4d33fe88381b813f4281b9b61881b74a0526d072 to /var/lib/mock/fedora-43-ppc64le-bootstrap-1769509389.082718/root
INFO: mounting 18e411c14bbe0ba80799508c4d33fe88381b813f4281b9b61881b74a0526d072 with podman image mount
INFO: image 18e411c14bbe0ba80799508c4d33fe88381b813f4281b9b61881b74a0526d072 as /var/lib/containers/storage/overlay/3e5bc801b11285f12ca0c1537e78755bcba25dfc88a470a8ae2284b929149385/merged
INFO: umounting image 18e411c14bbe0ba80799508c4d33fe88381b813f4281b9b61881b74a0526d072 (/var/lib/containers/storage/overlay/3e5bc801b11285f12ca0c1537e78755bcba25dfc88a470a8ae2284b929149385/merged) with podman image umount
INFO: Removing image mock-bootstrap-d91a7f98-1b23-4442-b000-a6878e36b85a
INFO: Package manager dnf5 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/fedora-43-ppc64le-1769509389.082718/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 dnf5 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-6.0.1-1.fc43.ppc64le
  rpm-sequoia-1.10.0-1.fc43.ppc64le
  dnf5-5.2.17.0-2.fc43.ppc64le
  dnf5-plugins-5.2.17.0-2.fc43.ppc64le
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 Copr repository                        100% | 132.0   B/s |   3.9 KiB |  00m31s
 updates                                100% | 337.5 KiB/s |  20.2 MiB |  01m01s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
 fedora                                 100% | 509.8 KiB/s |  33.3 MiB |  01m07s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
Repositories loaded.
Package                            Arch    Version                     Repository      Size
Installing group/module packages:
 bash                              ppc64le 5.3.0-2.fc43                fedora       8.9 MiB
 bzip2                             ppc64le 1.0.8-21.fc43               fedora     171.2 KiB
 coreutils                         ppc64le 9.7-7.fc43                  updates      9.4 MiB
 cpio                              ppc64le 2.15-6.fc43                 fedora       1.2 MiB
 diffutils                         ppc64le 3.12-3.fc43                 fedora       1.7 MiB
 fedora-release-common             noarch  43-25                       fedora      20.6 KiB
 findutils                         ppc64le 1:4.10.0-6.fc43             fedora       2.0 MiB
 gawk                              ppc64le 5.3.2-2.fc43                fedora       2.8 MiB
 glibc-minimal-langpack            ppc64le 2.42-9.fc43                 updates      0.0   B
 grep                              ppc64le 3.12-2.fc43                 fedora       1.0 MiB
 gzip                              ppc64le 1.13-4.fc43                 fedora     424.6 KiB
 info                              ppc64le 7.2-6.fc43                  fedora     485.5 KiB
 patch                             ppc64le 2.8-2.fc43                  fedora     262.5 KiB
 redhat-rpm-config                 noarch  343-11.fc43                 fedora     182.9 KiB
 rpm-build                         ppc64le 6.0.1-1.fc43                updates    663.4 KiB
 sed                               ppc64le 4.9-5.fc43                  fedora     937.1 KiB
 shadow-utils                      ppc64le 2:4.18.0-3.fc43             fedora       4.8 MiB
 tar                               ppc64le 2:1.35-6.fc43               fedora       3.1 MiB
 unzip                             ppc64le 6.0-67.fc43                 fedora     533.9 KiB
 util-linux                        ppc64le 2.41.3-7.fc43               updates      6.9 MiB
 which                             ppc64le 2.23-3.fc43                 fedora     123.3 KiB
 xz                                ppc64le 1:5.8.1-4.fc43              updates      1.4 MiB
Installing dependencies:
 add-determinism                   ppc64le 0.6.0-2.fc43                fedora       2.5 MiB
 alternatives                      ppc64le 1.33-3.fc43                 updates     90.1 KiB
 ansible-srpm-macros               noarch  1-18.1.fc43                 fedora      35.7 KiB
 audit-libs                        ppc64le 4.1.2-2.fc43                updates    550.5 KiB
 binutils                          ppc64le 2.45.1-4.fc43               updates     33.1 MiB
 build-reproducibility-srpm-macros noarch  0.6.0-2.fc43                fedora     735.0   B
 bzip2-libs                        ppc64le 1.0.8-21.fc43               fedora     136.5 KiB
 ca-certificates                   noarch  2025.2.80_v9.0.304-1.1.fc43 fedora       2.7 MiB
 coreutils-common                  ppc64le 9.7-7.fc43                  updates     11.3 MiB
 crypto-policies                   noarch  20251125-1.git63291f8.fc43  updates    147.1 KiB
 curl                              ppc64le 8.15.0-5.fc43               updates    521.5 KiB
 cyrus-sasl-lib                    ppc64le 2.1.28-33.fc43              fedora       2.9 MiB
 debugedit                         ppc64le 5.2-3.fc43                  fedora     381.6 KiB
 dwz                               ppc64le 0.16-2.fc43                 fedora     386.6 KiB
 ed                                ppc64le 1.22.2-1.fc43               fedora     155.9 KiB
 efi-srpm-macros                   noarch  6-4.fc43                    fedora      40.1 KiB
 elfutils                          ppc64le 0.194-1.fc43                updates      3.4 MiB
 elfutils-debuginfod-client        ppc64le 0.194-1.fc43                updates    143.5 KiB
 elfutils-default-yama-scope       noarch  0.194-1.fc43                updates      1.8 KiB
 elfutils-libelf                   ppc64le 0.194-1.fc43                updates      1.2 MiB
 elfutils-libs                     ppc64le 0.194-1.fc43                updates    874.6 KiB
 fedora-gpg-keys                   noarch  43-1                        fedora     131.2 KiB
 fedora-release                    noarch  43-25                       fedora       0.0   B
 fedora-release-identity-basic     noarch  43-25                       fedora     631.0   B
 fedora-repos                      noarch  43-1                        fedora       4.9 KiB
 file                              ppc64le 5.46-8.fc43                 fedora     140.1 KiB
 file-libs                         ppc64le 5.46-8.fc43                 fedora      11.9 MiB
 filesystem                        ppc64le 3.18-50.fc43                fedora     112.0   B
 filesystem-srpm-macros            noarch  3.18-50.fc43                fedora      38.2 KiB
 fonts-srpm-macros                 noarch  1:2.0.5-23.fc43             fedora      55.8 KiB
 forge-srpm-macros                 noarch  0.4.0-3.fc43                fedora      38.9 KiB
 fpc-srpm-macros                   noarch  1.3-15.fc43                 fedora     144.0   B
 gap-srpm-macros                   noarch  2-1.fc43                    fedora       2.1 KiB
 gdb-minimal                       ppc64le 17.1-1.fc43                 updates     16.1 MiB
 gdbm-libs                         ppc64le 1:1.23-10.fc43              fedora     233.5 KiB
 ghc-srpm-macros                   noarch  1.9.2-3.fc43                fedora     779.0   B
 glibc                             ppc64le 2.42-9.fc43                 updates     11.6 MiB
 glibc-common                      ppc64le 2.42-9.fc43                 updates      1.5 MiB
 glibc-gconv-extra                 ppc64le 2.42-9.fc43                 updates     18.5 MiB
 gmp                               ppc64le 1:6.3.0-4.fc43              fedora     786.2 KiB
 gnat-srpm-macros                  noarch  7-1.fc43                    updates      1.0 KiB
 gnulib-l10n                       noarch  20241231-1.fc43             fedora     655.0 KiB
 gnupg2                            ppc64le 2.4.9-4.fc43                updates      6.9 MiB
 gnupg2-dirmngr                    ppc64le 2.4.9-4.fc43                updates    838.1 KiB
 gnupg2-gpg-agent                  ppc64le 2.4.9-4.fc43                updates    975.0 KiB
 gnupg2-gpgconf                    ppc64le 2.4.9-4.fc43                updates    321.8 KiB
 gnupg2-keyboxd                    ppc64le 2.4.9-4.fc43                updates    297.2 KiB
 gnupg2-verify                     ppc64le 2.4.9-4.fc43                updates    428.3 KiB
 gnutls                            ppc64le 3.8.11-5.fc43               updates      4.1 MiB
 go-srpm-macros                    noarch  3.8.0-1.fc43                fedora      61.9 KiB
 gpgverify                         noarch  2.2-3.fc43                  fedora       8.7 KiB
 ima-evm-utils-libs                ppc64le 1.6.2-6.fc43                fedora      92.6 KiB
 jansson                           ppc64le 2.14-3.fc43                 fedora     157.0 KiB
 java-srpm-macros                  noarch  1-7.fc43                    fedora     870.0   B
 json-c                            ppc64le 0.18-7.fc43                 fedora     138.6 KiB
 kernel-srpm-macros                noarch  1.0-27.fc43                 fedora       1.9 KiB
 keyutils-libs                     ppc64le 1.6.3-6.fc43                fedora      98.0 KiB
 krb5-libs                         ppc64le 1.21.3-7.fc43               fedora       3.0 MiB
 libacl                            ppc64le 2.3.2-4.fc43                fedora      67.6 KiB
 libarchive                        ppc64le 3.8.4-1.fc43                updates      1.3 MiB
 libassuan                         ppc64le 2.5.7-4.fc43                fedora     215.8 KiB
 libattr                           ppc64le 2.5.2-6.fc43                fedora      68.1 KiB
 libblkid                          ppc64le 2.41.3-7.fc43               updates    354.5 KiB
 libbrotli                         ppc64le 1.2.0-1.fc43                updates      1.0 MiB
 libcap                            ppc64le 2.76-3.fc43                 fedora     507.7 KiB
 libcap-ng                         ppc64le 0.8.5-8.fc43                fedora     160.3 KiB
 libcom_err                        ppc64le 1.47.3-2.fc43               fedora     111.0 KiB
 libcurl                           ppc64le 8.15.0-5.fc43               updates      1.1 MiB
 libeconf                          ppc64le 0.7.9-2.fc43                fedora      80.8 KiB
 libevent                          ppc64le 2.1.12-16.fc43              fedora       1.2 MiB
 libfdisk                          ppc64le 2.41.3-7.fc43               updates    483.0 KiB
 libffi                            ppc64le 3.5.2-1.fc43                updates    347.7 KiB
 libfsverity                       ppc64le 1.6-3.fc43                  fedora      68.1 KiB
 libgcc                            ppc64le 15.2.1-5.fc43               updates    286.4 KiB
 libgcrypt                         ppc64le 1.11.1-3.fc43               updates      1.5 MiB
 libgomp                           ppc64le 15.2.1-5.fc43               updates    645.2 KiB
 libgpg-error                      ppc64le 1.55-2.fc43                 fedora       1.0 MiB
 libidn2                           ppc64le 2.3.8-2.fc43                fedora     560.2 KiB
 libksba                           ppc64le 1.6.7-4.fc43                fedora     526.5 KiB
 liblastlog2                       ppc64le 2.41.3-7.fc43               updates    137.4 KiB
 libmount                          ppc64le 2.41.3-7.fc43               updates    548.3 KiB
 libnghttp2                        ppc64le 1.66.0-2.fc43               fedora     197.9 KiB
 libpkgconf                        ppc64le 2.3.0-3.fc43                fedora     133.9 KiB
 libpsl                            ppc64le 0.21.5-6.fc43               fedora     132.1 KiB
 librtas                           ppc64le 2.0.6-4.fc43                fedora     305.4 KiB
 libselinux                        ppc64le 3.9-5.fc43                  fedora     265.1 KiB
 libsemanage                       ppc64le 3.9-4.fc43                  fedora     423.9 KiB
 libsepol                          ppc64le 3.9-2.fc43                  fedora       1.0 MiB
 libsmartcols                      ppc64le 2.41.3-7.fc43               updates    289.5 KiB
 libssh                            ppc64le 0.11.3-1.fc43               fedora     715.2 KiB
 libssh-config                     noarch  0.11.3-1.fc43               fedora     277.0   B
 libstdc++                         ppc64le 15.2.1-5.fc43               updates      3.9 MiB
 libtasn1                          ppc64le 4.20.0-2.fc43               fedora     220.0 KiB
 libtool-ltdl                      ppc64le 2.5.4-8.fc43                updates     93.9 KiB
 libunistring                      ppc64le 1.1-10.fc43                 fedora       1.9 MiB
 libusb1                           ppc64le 1.0.29-4.fc43               fedora     242.8 KiB
 libuuid                           ppc64le 2.41.3-7.fc43               updates     69.3 KiB
 libverto                          ppc64le 0.3.2-11.fc43               fedora      69.1 KiB
 libxcrypt                         ppc64le 4.5.2-1.fc43                updates    337.0 KiB
 libxml2                           ppc64le 2.12.10-5.fc43              fedora       2.3 MiB
 libzstd                           ppc64le 1.5.7-2.fc43                fedora     923.8 KiB
 lua-libs                          ppc64le 5.4.8-4.fc43                updates    393.8 KiB
 lua-srpm-macros                   noarch  1-16.fc43                   fedora       1.3 KiB
 lz4-libs                          ppc64le 1.10.0-3.fc43               fedora     261.1 KiB
 mpfr                              ppc64le 4.2.2-2.fc43                fedora     913.7 KiB
 ncurses-base                      noarch  6.5-7.20250614.fc43         fedora     328.1 KiB
 ncurses-libs                      ppc64le 6.5-7.20250614.fc43         fedora       1.5 MiB
 nettle                            ppc64le 3.10.1-2.fc43               fedora     957.8 KiB
 npth                              ppc64le 1.8-3.fc43                  fedora      93.1 KiB
 ocaml-srpm-macros                 noarch  11-2.fc43                   fedora       1.9 KiB
 openblas-srpm-macros              noarch  2-20.fc43                   fedora     112.0   B
 openldap                          ppc64le 2.6.10-4.fc43               fedora     889.9 KiB
 openssl-libs                      ppc64le 1:3.5.4-1.fc43              updates      9.0 MiB
 p11-kit                           ppc64le 0.25.8-1.fc43               fedora       2.9 MiB
 p11-kit-trust                     ppc64le 0.25.8-1.fc43               fedora     594.1 KiB
 package-notes-srpm-macros         noarch  0.5-14.fc43                 fedora       1.6 KiB
 pam-libs                          ppc64le 1.7.1-4.fc43                updates    286.3 KiB
 pcre2                             ppc64le 10.47-1.fc43                updates    842.0 KiB
 pcre2-syntax                      noarch  10.47-1.fc43                updates    281.9 KiB
 perl-srpm-macros                  noarch  1-60.fc43                   fedora     861.0   B
 pkgconf                           ppc64le 2.3.0-3.fc43                fedora     112.3 KiB
 pkgconf-m4                        noarch  2.3.0-3.fc43                fedora      14.4 KiB
 pkgconf-pkg-config                ppc64le 2.3.0-3.fc43                fedora     990.0   B
 popt                              ppc64le 1.19-9.fc43                 fedora     208.7 KiB
 publicsuffix-list-dafsa           noarch  20260116-1.fc43             updates     70.4 KiB
 pyproject-srpm-macros             noarch  1.18.6-1.fc43               updates      1.9 KiB
 python-srpm-macros                noarch  3.14-5.fc43                 fedora      51.5 KiB
 qt5-srpm-macros                   noarch  5.15.18-1.fc43              updates    500.0   B
 qt6-srpm-macros                   noarch  6.10.1-1.fc43               updates    464.0   B
 readline                          ppc64le 8.3-2.fc43                  fedora     627.5 KiB
 rpm                               ppc64le 6.0.1-1.fc43                updates      4.2 MiB
 rpm-build-libs                    ppc64le 6.0.1-1.fc43                updates    328.0 KiB
 rpm-libs                          ppc64le 6.0.1-1.fc43                updates      1.2 MiB
 rpm-sequoia                       ppc64le 1.10.0-1.fc43               updates      4.9 MiB
 rpm-sign-libs                     ppc64le 6.0.1-1.fc43                updates     67.6 KiB
 rust-srpm-macros                  noarch  28.4-1.fc43                 updates      5.5 KiB
 setup                             noarch  2.15.0-26.fc43              fedora     725.0 KiB
 sqlite-libs                       ppc64le 3.50.2-2.fc43               fedora       1.9 MiB
 systemd-libs                      ppc64le 258.3-2.fc43                updates      3.0 MiB
 systemd-standalone-sysusers       ppc64le 258.3-2.fc43                updates    393.5 KiB
 tpm2-tss                          ppc64le 4.1.3-8.fc43                fedora       2.5 MiB
 tree-sitter-srpm-macros           noarch  0.4.2-1.fc43                fedora       8.3 KiB
 util-linux-core                   ppc64le 2.41.3-7.fc43               updates      2.5 MiB
 xxhash-libs                       ppc64le 0.8.3-3.fc43                fedora      85.6 KiB
 xz-libs                           ppc64le 1:5.8.1-4.fc43              updates    265.3 KiB
 zig-srpm-macros                   noarch  1-5.fc43                    fedora       1.1 KiB
 zip                               ppc64le 3.0-44.fc43                 fedora     889.8 KiB
 zlib-ng-compat                    ppc64le 2.3.2-2.fc43                updates    197.4 KiB
 zstd                              ppc64le 1.5.7-2.fc43                fedora       1.9 MiB
Installing groups:
 Buildsystem building group                                                                

Transaction Summary:
 Installing:       171 packages

Total size of inbound packages is 65 MiB. Need to download 65 MiB.
After this operation, 257 MiB extra will be used (install 257 MiB, remove 0 B).
[  1/171] bzip2-0:1.0.8-21.fc43.ppc64le 100% |   1.7 KiB/s |  52.9 KiB |  00m31s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
[  2/171] cpio-0:2.15-6.fc43.ppc64le    100% |   9.7 KiB/s | 300.4 KiB |  00m31s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
[  3/171] fedora-release-common-0:43-25 100% | 187.6 KiB/s |  24.6 KiB |  00m00s
[  4/171] diffutils-0:3.12-3.fc43.ppc64 100% | 779.5 KiB/s | 404.6 KiB |  00m01s
[  5/171] bash-0:5.3.0-2.fc43.ppc64le   100% |  63.5 KiB/s |   2.0 MiB |  00m32s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
[  6/171] gawk-0:5.3.2-2.fc43.ppc64le   100% |   3.0 MiB/s |   1.2 MiB |  00m00s
[  7/171] grep-0:3.12-2.fc43.ppc64le    100% |   2.2 MiB/s | 309.2 KiB |  00m00s
[  8/171] gzip-0:1.13-4.fc43.ppc64le    100% |   1.3 MiB/s | 174.2 KiB |  00m00s
[  9/171] info-0:7.2-6.fc43.ppc64le     100% |   1.5 MiB/s | 202.9 KiB |  00m00s
[ 10/171] patch-0:2.8-2.fc43.ppc64le    100% | 938.3 KiB/s | 123.9 KiB |  00m00s
[ 11/171] findutils-1:4.10.0-6.fc43.ppc 100% | 774.7 KiB/s | 587.3 KiB |  00m01s
[ 12/171] redhat-rpm-config-0:343-11.fc 100% | 604.0 KiB/s |  79.1 KiB |  00m00s
[ 13/171] sed-0:4.9-5.fc43.ppc64le      100% |   2.4 MiB/s | 322.7 KiB |  00m00s
[ 14/171] tar-2:1.35-6.fc43.ppc64le     100% |   6.0 MiB/s | 883.9 KiB |  00m00s
[ 15/171] unzip-0:6.0-67.fc43.ppc64le   100% |   1.4 MiB/s | 191.2 KiB |  00m00s
[ 16/171] shadow-utils-2:4.18.0-3.fc43. 100% |   4.7 MiB/s |   1.3 MiB |  00m00s
[ 17/171] which-0:2.23-3.fc43.ppc64le   100% | 330.8 KiB/s |  43.0 KiB |  00m00s
[ 18/171] glibc-minimal-langpack-0:2.42 100% |   1.4 KiB/s |  40.8 KiB |  00m30s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
[ 19/171] coreutils-0:9.7-7.fc43.ppc64l 100% |  41.5 KiB/s |   1.2 MiB |  00m30s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
[ 20/171] util-linux-0:2.41.3-7.fc43.pp 100% |  16.3 MiB/s |   1.3 MiB |  00m00s
[ 21/171] xz-1:5.8.1-4.fc43.ppc64le     100% |  19.4 MiB/s | 577.2 KiB |  00m00s
[ 22/171] rpm-build-0:6.0.1-1.fc43.ppc6 100% |   5.3 KiB/s | 160.6 KiB |  00m30s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
[ 23/171] bzip2-libs-0:1.0.8-21.fc43.pp 100% | 124.8 KiB/s |  49.3 KiB |  00m00s
[ 24/171] fedora-repos-0:43-1.noarch    100% |  69.6 KiB/s |   9.1 KiB |  00m00s
[ 25/171] libselinux-0:3.9-5.fc43.ppc64 100% | 414.9 KiB/s | 112.4 KiB |  00m00s
[ 26/171] ncurses-libs-0:6.5-7.20250614 100% | 393.7 KiB/s | 383.4 KiB |  00m01s
[ 27/171] gmp-1:6.3.0-4.fc43.ppc64le    100% | 740.4 KiB/s | 321.3 KiB |  00m00s
[ 28/171] mpfr-0:4.2.2-2.fc43.ppc64le   100% |   1.3 MiB/s | 362.2 KiB |  00m00s
[ 29/171] filesystem-0:3.18-50.fc43.ppc 100% |   1.0 MiB/s |   1.3 MiB |  00m01s
[ 30/171] readline-0:8.3-2.fc43.ppc64le 100% |   1.7 MiB/s | 243.7 KiB |  00m00s
[ 31/171] ed-0:1.22.2-1.fc43.ppc64le    100% | 650.1 KiB/s |  86.5 KiB |  00m00s
[ 32/171] libattr-0:2.5.2-6.fc43.ppc64l 100% | 141.5 KiB/s |  18.7 KiB |  00m00s
[ 33/171] ansible-srpm-macros-0:1-18.1. 100% | 150.8 KiB/s |  19.9 KiB |  00m00s
[ 34/171] build-reproducibility-srpm-ma 100% |  92.4 KiB/s |  11.8 KiB |  00m00s
[ 35/171] dwz-0:0.16-2.fc43.ppc64le     100% |   1.1 MiB/s | 145.5 KiB |  00m00s
[ 36/171] efi-srpm-macros-0:6-4.fc43.no 100% | 170.9 KiB/s |  22.4 KiB |  00m00s
[ 37/171] file-0:5.46-8.fc43.ppc64le    100% | 385.0 KiB/s |  49.7 KiB |  00m00s
[ 38/171] filesystem-srpm-macros-0:3.18 100% | 201.6 KiB/s |  26.4 KiB |  00m00s
[ 39/171] fonts-srpm-macros-1:2.0.5-23. 100% | 205.9 KiB/s |  27.2 KiB |  00m00s
[ 40/171] forge-srpm-macros-0:0.4.0-3.f 100% | 156.9 KiB/s |  20.1 KiB |  00m00s
[ 41/171] fpc-srpm-macros-0:1.3-15.fc43 100% |  60.2 KiB/s |   7.9 KiB |  00m00s
[ 42/171] gap-srpm-macros-0:2-1.fc43.no 100% |  68.5 KiB/s |   9.0 KiB |  00m00s
[ 43/171] ghc-srpm-macros-0:1.9.2-3.fc4 100% |  67.8 KiB/s |   8.7 KiB |  00m00s
[ 44/171] go-srpm-macros-0:3.8.0-1.fc43 100% | 216.1 KiB/s |  28.3 KiB |  00m00s
[ 45/171] java-srpm-macros-0:1-7.fc43.n 100% |  61.6 KiB/s |   7.9 KiB |  00m00s
[ 46/171] kernel-srpm-macros-0:1.0-27.f 100% |  68.1 KiB/s |   8.9 KiB |  00m00s
[ 47/171] lua-srpm-macros-0:1-16.fc43.n 100% |  66.8 KiB/s |   8.8 KiB |  00m00s
[ 48/171] ocaml-srpm-macros-0:11-2.fc43 100% |  71.8 KiB/s |   9.3 KiB |  00m00s
[ 49/171] openblas-srpm-macros-0:2-20.f 100% |  57.5 KiB/s |   7.6 KiB |  00m00s
[ 50/171] package-notes-srpm-macros-0:0 100% |  69.1 KiB/s |   9.0 KiB |  00m00s
[ 51/171] perl-srpm-macros-0:1-60.fc43. 100% |  64.3 KiB/s |   8.3 KiB |  00m00s
[ 52/171] python-srpm-macros-0:3.14-5.f 100% | 177.1 KiB/s |  23.4 KiB |  00m00s
[ 53/171] tree-sitter-srpm-macros-0:0.4 100% | 101.9 KiB/s |  13.4 KiB |  00m00s
[ 54/171] zig-srpm-macros-0:1-5.fc43.no 100% |  65.4 KiB/s |   8.4 KiB |  00m00s
[ 55/171] zip-0:3.0-44.fc43.ppc64le     100% |   1.9 MiB/s | 275.0 KiB |  00m00s
[ 56/171] libacl-0:2.3.2-4.fc43.ppc64le 100% | 199.5 KiB/s |  26.5 KiB |  00m00s
[ 57/171] libeconf-0:0.7.9-2.fc43.ppc64 100% | 314.7 KiB/s |  40.3 KiB |  00m00s
[ 58/171] libsemanage-0:3.9-4.fc43.ppc6 100% |   1.0 MiB/s | 135.1 KiB |  00m00s
[ 59/171] setup-0:2.15.0-26.fc43.noarch 100% |   1.1 MiB/s | 157.3 KiB |  00m00s
[ 60/171] coreutils-common-0:9.7-7.fc43 100% |  19.6 MiB/s |   2.1 MiB |  00m00s
[ 61/171] glibc-common-0:2.42-9.fc43.pp 100% |  20.8 MiB/s | 341.1 KiB |  00m00s
[ 62/171] rpm-0:6.0.1-1.fc43.ppc64le    100% |  33.3 MiB/s | 579.5 KiB |  00m00s
[ 63/171] libcap-0:2.76-3.fc43.ppc64le  100% | 728.4 KiB/s |  94.7 KiB |  00m00s
[ 64/171] glibc-0:2.42-9.fc43.ppc64le   100% |  26.5 MiB/s |   3.1 MiB |  00m00s
[ 65/171] debugedit-0:5.2-3.fc43.ppc64l 100% | 676.3 KiB/s |  89.3 KiB |  00m00s
[ 66/171] pkgconf-pkg-config-0:2.3.0-3. 100% |  74.5 KiB/s |   9.5 KiB |  00m00s
[ 67/171] libblkid-0:2.41.3-7.fc43.ppc6 100% |  10.0 MiB/s | 143.0 KiB |  00m00s
[ 68/171] libfdisk-0:2.41.3-7.fc43.ppc6 100% |  12.4 MiB/s | 177.8 KiB |  00m00s
[ 69/171] liblastlog2-0:2.41.3-7.fc43.p 100% |   1.8 MiB/s |  24.3 KiB |  00m00s
[ 70/171] libmount-0:2.41.3-7.fc43.ppc6 100% |  13.1 MiB/s | 187.4 KiB |  00m00s
[ 71/171] popt-0:1.19-9.fc43.ppc64le    100% | 528.7 KiB/s |  70.3 KiB |  00m00s
[ 72/171] libsmartcols-0:2.41.3-7.fc43. 100% |   8.3 MiB/s | 110.8 KiB |  00m00s
[ 73/171] libuuid-0:2.41.3-7.fc43.ppc64 100% |   2.3 MiB/s |  27.9 KiB |  00m00s
[ 74/171] util-linux-core-0:2.41.3-7.fc 100% |  34.0 MiB/s | 591.8 KiB |  00m00s
[ 75/171] libcap-ng-0:0.8.5-8.fc43.ppc6 100% | 261.1 KiB/s |  33.4 KiB |  00m00s
[ 76/171] xz-libs-1:5.8.1-4.fc43.ppc64l 100% |   8.8 MiB/s | 126.5 KiB |  00m00s
[ 77/171] librtas-0:2.0.6-4.fc43.ppc64l 100% | 613.2 KiB/s |  80.9 KiB |  00m00s
[ 78/171] ncurses-base-0:6.5-7.20250614 100% | 678.6 KiB/s |  88.2 KiB |  00m00s
[ 79/171] fedora-gpg-keys-0:43-1.noarch 100% |   1.0 MiB/s | 138.9 KiB |  00m00s
[ 80/171] zstd-0:1.5.7-2.fc43.ppc64le   100% |   1.0 MiB/s | 527.4 KiB |  00m01s
[ 81/171] libsepol-0:3.9-2.fc43.ppc64le 100% |   1.4 MiB/s | 380.8 KiB |  00m00s
[ 82/171] gnulib-l10n-0:20241231-1.fc43 100% |   1.1 MiB/s | 150.2 KiB |  00m00s
[ 83/171] add-determinism-0:0.6.0-2.fc4 100% |   2.3 MiB/s | 957.8 KiB |  00m00s
[ 84/171] glibc-gconv-extra-0:2.42-9.fc 100% |  33.0 MiB/s |   1.6 MiB |  00m00s
[ 85/171] pkgconf-0:2.3.0-3.fc43.ppc64l 100% | 348.1 KiB/s |  45.2 KiB |  00m00s
[ 86/171] pkgconf-m4-0:2.3.0-3.fc43.noa 100% | 107.0 KiB/s |  13.9 KiB |  00m00s
[ 87/171] lz4-libs-0:1.10.0-3.fc43.ppc6 100% | 785.9 KiB/s | 103.0 KiB |  00m00s
[ 88/171] libpkgconf-0:2.3.0-3.fc43.ppc 100% | 332.2 KiB/s |  42.9 KiB |  00m00s
[ 89/171] rpm-libs-0:6.0.1-1.fc43.ppc64 100% |  25.6 MiB/s | 445.5 KiB |  00m00s
[ 90/171] file-libs-0:5.46-8.fc43.ppc64 100% |   1.3 MiB/s | 862.2 KiB |  00m01s
[ 91/171] rpm-build-libs-0:6.0.1-1.fc43 100% |   6.2 MiB/s | 133.6 KiB |  00m00s
[ 92/171] rpm-sign-libs-0:6.0.1-1.fc43. 100% | 982.2 KiB/s |  28.5 KiB |  00m00s
[ 93/171] sqlite-libs-0:3.50.2-2.fc43.p 100% |   2.1 MiB/s | 870.0 KiB |  00m00s
[ 94/171] ima-evm-utils-libs-0:1.6.2-6. 100% | 235.3 KiB/s |  30.1 KiB |  00m00s
[ 95/171] libzstd-0:1.5.7-2.fc43.ppc64l 100% |   1.3 MiB/s | 356.9 KiB |  00m00s
[ 96/171] libfsverity-0:1.6-3.fc43.ppc6 100% | 146.0 KiB/s |  19.1 KiB |  00m00s
[ 97/171] json-c-0:0.18-7.fc43.ppc64le  100% | 380.8 KiB/s |  49.5 KiB |  00m00s
[ 98/171] libgcc-0:15.2.1-5.fc43.ppc64l 100% |   8.2 MiB/s | 117.8 KiB |  00m00s
[ 99/171] libusb1-0:1.0.29-4.fc43.ppc64 100% | 646.9 KiB/s |  85.4 KiB |  00m00s
[100/171] libstdc++-0:15.2.1-5.fc43.ppc 100% |  33.5 MiB/s |   1.0 MiB |  00m00s
[101/171] tpm2-tss-0:4.1.3-8.fc43.ppc64 100% |   1.5 MiB/s | 399.4 KiB |  00m00s
[102/171] zlib-ng-compat-0:2.3.2-2.fc43 100% |   2.3 MiB/s |  90.7 KiB |  00m00s
[103/171] openssl-libs-1:3.5.4-1.fc43.p 100% |  65.9 MiB/s |   2.8 MiB |  00m00s
[104/171] p11-kit-trust-0:0.25.8-1.fc43 100% |   1.1 MiB/s | 156.5 KiB |  00m00s
[105/171] libtasn1-0:4.20.0-2.fc43.ppc6 100% | 610.3 KiB/s |  81.2 KiB |  00m00s
[106/171] audit-libs-0:4.1.2-2.fc43.ppc 100% |  10.1 MiB/s | 155.0 KiB |  00m00s
[107/171] libxcrypt-0:4.5.2-1.fc43.ppc6 100% |   9.1 MiB/s | 139.5 KiB |  00m00s
[108/171] pam-libs-0:1.7.1-4.fc43.ppc64 100% |   4.4 MiB/s |  63.1 KiB |  00m00s
[109/171] p11-kit-0:0.25.8-1.fc43.ppc64 100% |   1.3 MiB/s | 513.5 KiB |  00m00s
[110/171] gnat-srpm-macros-0:7-1.fc43.n 100% | 188.2 KiB/s |   8.7 KiB |  00m00s
[111/171] qt5-srpm-macros-0:5.15.18-1.f 100% | 452.8 KiB/s |   8.6 KiB |  00m00s
[112/171] pyproject-srpm-macros-0:1.18. 100% | 637.7 KiB/s |  13.4 KiB |  00m00s
[113/171] rust-srpm-macros-0:28.4-1.fc4 100% | 602.6 KiB/s |  10.8 KiB |  00m00s
[114/171] qt6-srpm-macros-0:6.10.1-1.fc 100% | 406.8 KiB/s |   9.4 KiB |  00m00s
[115/171] alternatives-0:1.33-3.fc43.pp 100% |   3.0 MiB/s |  43.6 KiB |  00m00s
[116/171] libffi-0:3.5.2-1.fc43.ppc64le 100% |   3.2 MiB/s |  42.0 KiB |  00m00s
[117/171] pcre2-0:10.47-1.fc43.ppc64le  100% |  18.4 MiB/s | 282.2 KiB |  00m00s
[118/171] systemd-libs-0:258.3-2.fc43.p 100% |  15.5 MiB/s | 886.8 KiB |  00m00s
[119/171] pcre2-syntax-0:10.47-1.fc43.n 100% |   4.0 MiB/s | 164.7 KiB |  00m00s
[120/171] elfutils-libelf-0:0.194-1.fc4 100% |  12.9 MiB/s | 212.0 KiB |  00m00s
[121/171] elfutils-libs-0:0.194-1.fc43. 100% |  19.0 MiB/s | 311.2 KiB |  00m00s
[122/171] elfutils-debuginfod-client-0: 100% |   3.8 MiB/s |  50.1 KiB |  00m00s
[123/171] elfutils-0:0.194-1.fc43.ppc64 100% |  10.5 MiB/s | 572.2 KiB |  00m00s
[124/171] jansson-0:2.14-3.fc43.ppc64le 100% | 389.9 KiB/s |  50.7 KiB |  00m00s
[125/171] gnupg2-0:2.4.9-4.fc43.ppc64le 100% |  22.9 MiB/s |   1.7 MiB |  00m00s
[126/171] ca-certificates-0:2025.2.80_v 100% |   1.2 MiB/s | 975.4 KiB |  00m01s
[127/171] gnupg2-dirmngr-0:2.4.9-4.fc43 100% |  10.0 MiB/s | 316.1 KiB |  00m00s
[128/171] binutils-0:2.45.1-4.fc43.ppc6 100% |  20.5 MiB/s |   6.7 MiB |  00m00s
[129/171] gnupg2-gpg-agent-0:2.4.9-4.fc 100% |   6.5 MiB/s | 306.3 KiB |  00m00s
[130/171] gnupg2-gpgconf-0:2.4.9-4.fc43 100% |   5.3 MiB/s | 125.2 KiB |  00m00s
[131/171] gnupg2-keyboxd-0:2.4.9-4.fc43 100% |   4.4 MiB/s | 103.8 KiB |  00m00s
[132/171] gnupg2-verify-0:2.4.9-4.fc43. 100% |   8.7 MiB/s | 186.2 KiB |  00m00s
[133/171] gpgverify-0:2.2-3.fc43.noarch 100% |  85.4 KiB/s |  11.1 KiB |  00m00s
[134/171] libassuan-0:2.5.7-4.fc43.ppc6 100% | 545.8 KiB/s |  71.5 KiB |  00m00s
[135/171] npth-0:1.8-3.fc43.ppc64le     100% | 193.7 KiB/s |  25.2 KiB |  00m00s
[136/171] libksba-0:1.6.7-4.fc43.ppc64l 100% |   1.3 MiB/s | 177.7 KiB |  00m00s
[137/171] libgpg-error-0:1.55-2.fc43.pp 100% | 962.3 KiB/s | 256.9 KiB |  00m00s
[138/171] openldap-0:2.6.10-4.fc43.ppc6 100% |   1.1 MiB/s | 289.8 KiB |  00m00s
[139/171] libevent-0:2.1.12-16.fc43.ppc 100% |   1.9 MiB/s | 274.4 KiB |  00m00s
[140/171] lua-libs-0:5.4.8-4.fc43.ppc64 100% |   9.7 MiB/s | 149.5 KiB |  00m00s
[141/171] rpm-sequoia-0:1.10.0-1.fc43.p 100% |  46.4 MiB/s |   1.6 MiB |  00m00s
[142/171] libgomp-0:15.2.1-5.fc43.ppc64 100% |  10.7 MiB/s | 392.7 KiB |  00m00s
[143/171] libarchive-0:3.8.4-1.fc43.ppc 100% |  28.5 MiB/s | 495.3 KiB |  00m00s
[144/171] gdbm-libs-1:1.23-10.fc43.ppc6 100% | 471.9 KiB/s |  61.8 KiB |  00m00s
[145/171] curl-0:8.15.0-5.fc43.ppc64le  100% |  14.5 MiB/s | 237.1 KiB |  00m00s
[146/171] crypto-policies-0:20251125-1. 100% |   4.2 MiB/s |  97.8 KiB |  00m00s
[147/171] libgcrypt-0:1.11.1-3.fc43.ppc 100% |  10.7 MiB/s | 666.4 KiB |  00m00s
[148/171] gnutls-0:3.8.11-5.fc43.ppc64l 100% |  57.0 MiB/s |   1.4 MiB |  00m00s
[149/171] libidn2-0:2.3.8-2.fc43.ppc64l 100% |   1.3 MiB/s | 177.3 KiB |  00m00s
[150/171] cyrus-sasl-lib-0:2.1.28-33.fc 100% |   1.4 MiB/s | 902.0 KiB |  00m01s
[151/171] libxml2-0:2.12.10-5.fc43.ppc6 100% |   1.9 MiB/s | 776.2 KiB |  00m00s
[152/171] elfutils-default-yama-scope-0 100% | 562.5 KiB/s |  12.4 KiB |  00m00s
[153/171] libtool-ltdl-0:2.5.4-8.fc43.p 100% |   3.0 MiB/s |  39.7 KiB |  00m00s
[154/171] fedora-release-0:43-25.noarch 100% | 103.0 KiB/s |  13.5 KiB |  00m00s
[155/171] fedora-release-identity-basic 100% | 108.8 KiB/s |  14.3 KiB |  00m00s
[156/171] nettle-0:3.10.1-2.fc43.ppc64l 100% |   1.2 MiB/s | 461.0 KiB |  00m00s
[157/171] libunistring-0:1.1-10.fc43.pp 100% |   1.1 MiB/s | 575.4 KiB |  00m01s
[158/171] gdb-minimal-0:17.1-1.fc43.ppc 100% |  29.5 MiB/s |   4.7 MiB |  00m00s
[159/171] systemd-standalone-sysusers-0 100% |   2.4 MiB/s | 154.0 KiB |  00m00s
[160/171] libcurl-0:8.15.0-5.fc43.ppc64 100% |  26.2 MiB/s | 456.7 KiB |  00m00s
[161/171] xxhash-libs-0:0.8.3-3.fc43.pp 100% | 290.7 KiB/s |  37.8 KiB |  00m00s
[162/171] libnghttp2-0:1.66.0-2.fc43.pp 100% | 600.9 KiB/s |  79.9 KiB |  00m00s
[163/171] libpsl-0:0.21.5-6.fc43.ppc64l 100% | 517.3 KiB/s |  66.7 KiB |  00m00s
[164/171] libssh-0:0.11.3-1.fc43.ppc64l 100% |   1.9 MiB/s | 266.5 KiB |  00m00s
[165/171] keyutils-libs-0:1.6.3-6.fc43. 100% | 252.3 KiB/s |  32.5 KiB |  00m00s
[166/171] libcom_err-0:1.47.3-2.fc43.pp 100% | 207.2 KiB/s |  27.1 KiB |  00m00s
[167/171] libverto-0:0.3.2-11.fc43.ppc6 100% | 171.0 KiB/s |  21.9 KiB |  00m00s
[168/171] publicsuffix-list-dafsa-0:202 100% |   2.9 MiB/s |  60.3 KiB |  00m00s
[169/171] libbrotli-0:1.2.0-1.fc43.ppc6 100% |  22.9 MiB/s | 398.8 KiB |  00m00s
[170/171] libssh-config-0:0.11.3-1.fc43 100% |  69.6 KiB/s |   9.1 KiB |  00m00s
[171/171] krb5-libs-0:1.21.3-7.fc43.ppc 100% |   1.3 MiB/s | 848.6 KiB |  00m01s
--------------------------------------------------------------------------------
[171/171] Total                         100% | 948.1 KiB/s |  64.6 MiB |  01m10s
Running transaction
Importing OpenPGP key 0x31645531:
 UserID     : "Fedora (43) <fedora-43-primary@fedoraproject.org>"
 Fingerprint: C6E7F081CF80E13146676E88829B606631645531
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary
The key was successfully imported.
[  1/173] Verify package files          100% | 166.0   B/s | 171.0   B |  00m01s
[  2/173] Prepare transaction           100% |   1.0 KiB/s | 171.0   B |  00m00s
[  3/173] Installing libgcc-0:15.2.1-5. 100% |  70.3 MiB/s | 288.1 KiB |  00m00s
[  4/173] Installing publicsuffix-list- 100% |  34.7 MiB/s |  71.1 KiB |  00m00s
[  5/173] Installing libssh-config-0:0. 100% | 796.9 KiB/s | 816.0   B |  00m00s
[  6/173] Installing fedora-release-ide 100% | 433.6 KiB/s | 888.0   B |  00m00s
[  7/173] Installing fedora-gpg-keys-0: 100% |  10.9 MiB/s | 179.0 KiB |  00m00s
[  8/173] Installing fedora-repos-0:43- 100% |   5.6 MiB/s |   5.7 KiB |  00m00s
[  9/173] Installing fedora-release-com 100% |   8.1 MiB/s |  24.9 KiB |  00m00s
[ 10/173] Installing fedora-release-0:4 100% |   7.1 KiB/s | 124.0   B |  00m00s
>>> Running sysusers scriptlet: setup-0:2.15.0-26.fc43.noarch                   
>>> Finished sysusers scriptlet: setup-0:2.15.0-26.fc43.noarch                  
>>> Scriptlet output:                                                           
>>> Creating group 'adm' with GID 4.                                            
>>> Creating group 'audio' with GID 63.                                         
>>> Creating group 'cdrom' with GID 11.                                         
>>> Creating group 'clock' with GID 103.                                        
>>> Creating group 'dialout' with GID 18.                                       
>>> Creating group 'disk' with GID 6.                                           
>>> Creating group 'floppy' with GID 19.                                        
>>> Creating group 'ftp' with GID 50.                                           
>>> Creating group 'games' with GID 20.                                         
>>> Creating group 'input' with GID 104.                                        
>>> Creating group 'kmem' with GID 9.                                           
>>> Creating group 'kvm' with GID 36.                                           
>>> Creating group 'lock' with GID 54.                                          
>>> Creating group 'lp' with GID 7.                                             
>>> Creating group 'mail' with GID 12.                                          
>>> Creating group 'man' with GID 15.                                           
>>> Creating group 'mem' with GID 8.                                            
>>> Creating group 'nobody' with GID 65534.                                     
>>> Creating group 'render' with GID 105.                                       
>>> Creating group 'root' with GID 0.                                           
>>> Creating group 'sgx' with GID 106.                                          
>>> Creating group 'sys' with GID 3.                                            
>>> Creating group 'tape' with GID 33.                                          
>>> Creating group 'tty' with GID 5.                                            
>>> Creating group 'users' with GID 100.                                        
>>> Creating group 'utmp' with GID 22.                                          
>>> Creating group 'video' with GID 39.                                         
>>> Creating group 'wheel' with GID 10.                                         
>>> Creating user 'adm' (adm) with UID 3 and GID 4.                             
>>> Creating group 'bin' with GID 1.                                            
>>> Creating user 'bin' (bin) with UID 1 and GID 1.                             
>>> Creating group 'daemon' with GID 2.                                         
>>> Creating user 'daemon' (daemon) with UID 2 and GID 2.                       
>>> Creating user 'ftp' (FTP User) with UID 14 and GID 50.                      
>>> Creating user 'games' (games) with UID 12 and GID 100.                      
>>> Creating user 'halt' (halt) with UID 7 and GID 0.                           
>>> Creating user 'lp' (lp) with UID 4 and GID 7.                               
>>> Creating user 'mail' (mail) with UID 8 and GID 12.                          
>>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534. 
>>> Creating user 'operator' (operator) with UID 11 and GID 0.                  
>>> Creating user 'root' (Super User) with UID 0 and GID 0.                     
>>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0.                   
>>> Creating user 'sync' (sync) with UID 5 and GID 0.                           
>>>                                                                             
[ 11/173] Installing setup-0:2.15.0-26. 100% |  14.3 MiB/s | 730.6 KiB |  00m00s
>>> [RPM] /etc/hosts created as /etc/hosts.rpmnew                               
[ 12/173] Installing filesystem-0:3.18- 100% | 733.6 KiB/s | 212.8 KiB |  00m00s
[ 13/173] Installing pcre2-syntax-0:10. 100% |  69.4 MiB/s | 284.3 KiB |  00m00s
[ 14/173] Installing rust-srpm-macros-0 100% |   6.2 MiB/s |   6.4 KiB |  00m00s
[ 15/173] Installing qt6-srpm-macros-0: 100% | 722.7 KiB/s | 740.0   B |  00m00s
[ 16/173] Installing qt5-srpm-macros-0: 100% | 757.8 KiB/s | 776.0   B |  00m00s
[ 17/173] Installing gnat-srpm-macros-0 100% |   1.2 MiB/s |   1.3 KiB |  00m00s
[ 18/173] Installing pkgconf-m4-0:2.3.0 100% |  14.5 MiB/s |  14.8 KiB |  00m00s
[ 19/173] Installing gnulib-l10n-0:2024 100% |  53.9 MiB/s | 661.9 KiB |  00m00s
[ 20/173] Installing coreutils-common-0 100% | 114.1 MiB/s |  11.3 MiB |  00m00s
[ 21/173] Installing ncurses-base-0:6.5 100% |  19.2 MiB/s | 353.5 KiB |  00m00s
[ 22/173] Installing bash-0:5.3.0-2.fc4 100% |  79.7 MiB/s |   8.9 MiB |  00m00s
[ 23/173] Installing glibc-common-0:2.4 100% |  26.5 MiB/s |   1.5 MiB |  00m00s
[ 24/173] Installing glibc-gconv-extra- 100% | 123.8 MiB/s |  18.6 MiB |  00m00s
[ 25/173] Installing glibc-0:2.42-9.fc4 100% |  79.3 MiB/s |  11.6 MiB |  00m00s
[ 26/173] Installing ncurses-libs-0:6.5 100% |  99.7 MiB/s |   1.5 MiB |  00m00s
[ 27/173] Installing glibc-minimal-lang 100% | 121.1 KiB/s | 124.0   B |  00m00s
[ 28/173] Installing zlib-ng-compat-0:2 100% |  64.5 MiB/s | 198.2 KiB |  00m00s
[ 29/173] Installing bzip2-libs-0:1.0.8 100% |  67.2 MiB/s | 137.7 KiB |  00m00s
[ 30/173] Installing libgpg-error-0:1.5 100% |  20.7 MiB/s |   1.0 MiB |  00m00s
[ 31/173] Installing libstdc++-0:15.2.1 100% | 126.0 MiB/s |   3.9 MiB |  00m00s
[ 32/173] Installing xz-libs-1:5.8.1-4. 100% |  65.0 MiB/s | 266.4 KiB |  00m00s
[ 33/173] Installing libassuan-0:2.5.7- 100% |  70.8 MiB/s | 217.6 KiB |  00m00s
[ 34/173] Installing libgcrypt-0:1.11.1 100% | 107.7 MiB/s |   1.5 MiB |  00m00s
[ 35/173] Installing readline-0:8.3-2.f 100% |  87.8 MiB/s | 629.7 KiB |  00m00s
[ 36/173] Installing gmp-1:6.3.0-4.fc43 100% |  96.2 MiB/s | 788.4 KiB |  00m00s
[ 37/173] Installing libuuid-0:2.41.3-7 100% |  34.3 MiB/s |  70.3 KiB |  00m00s
[ 38/173] Installing popt-0:1.19-9.fc43 100% |  26.3 MiB/s | 215.3 KiB |  00m00s
[ 39/173] Installing npth-0:1.8-3.fc43. 100% |  46.0 MiB/s |  94.2 KiB |  00m00s
[ 40/173] Installing libblkid-0:2.41.3- 100% |  86.8 MiB/s | 355.7 KiB |  00m00s
[ 41/173] Installing sqlite-libs-0:3.50 100% | 107.7 MiB/s |   1.9 MiB |  00m00s
[ 42/173] Installing libzstd-0:1.5.7-2. 100% | 100.4 MiB/s | 925.0 KiB |  00m00s
[ 43/173] Installing elfutils-libelf-0: 100% | 109.7 MiB/s |   1.2 MiB |  00m00s
[ 44/173] Installing libxcrypt-0:4.5.2- 100% |  66.4 MiB/s | 339.7 KiB |  00m00s
[ 45/173] Installing gnupg2-gpgconf-0:2 100% |   7.7 MiB/s | 323.9 KiB |  00m00s
[ 46/173] Installing libattr-0:2.5.2-6. 100% |  33.7 MiB/s |  69.1 KiB |  00m00s
[ 47/173] Installing libacl-0:2.3.2-4.f 100% |  33.4 MiB/s |  68.4 KiB |  00m00s
[ 48/173] Installing libtasn1-0:4.20.0- 100% |  54.2 MiB/s | 221.9 KiB |  00m00s
[ 49/173] Installing libunistring-0:1.1 100% | 117.0 MiB/s |   1.9 MiB |  00m00s
[ 50/173] Installing libidn2-0:2.3.8-2. 100% |  27.7 MiB/s | 566.4 KiB |  00m00s
[ 51/173] Installing crypto-policies-0: 100% |   9.9 MiB/s | 172.2 KiB |  00m00s
[ 52/173] Installing dwz-0:0.16-2.fc43. 100% |   9.2 MiB/s | 388.0 KiB |  00m00s
[ 53/173] Installing gnupg2-verify-0:2. 100% |  10.2 MiB/s | 429.7 KiB |  00m00s
[ 54/173] Installing mpfr-0:4.2.2-2.fc4 100% |  89.4 MiB/s | 915.3 KiB |  00m00s
[ 55/173] Installing gawk-0:5.3.2-2.fc4 100% |  44.2 MiB/s |   2.8 MiB |  00m00s
[ 56/173] Installing libksba-0:1.6.7-4. 100% |  86.1 MiB/s | 529.0 KiB |  00m00s
[ 57/173] Installing unzip-0:6.0-67.fc4 100% |  12.2 MiB/s | 537.4 KiB |  00m00s
[ 58/173] Installing file-libs-0:5.46-8 100% | 180.0 MiB/s |  11.9 MiB |  00m00s
[ 59/173] Installing file-0:5.46-8.fc43 100% |   3.5 MiB/s | 141.6 KiB |  00m00s
[ 60/173] Installing libeconf-0:0.7.9-2 100% |  40.3 MiB/s |  82.5 KiB |  00m00s
[ 61/173] Installing libsmartcols-0:2.4 100% |  70.9 MiB/s | 290.6 KiB |  00m00s
[ 62/173] Installing libcap-ng-0:0.8.5- 100% |  52.8 MiB/s | 162.1 KiB |  00m00s
[ 63/173] Installing audit-libs-0:4.1.2 100% |  90.0 MiB/s | 553.2 KiB |  00m00s
[ 64/173] Installing pam-libs-0:1.7.1-4 100% |  70.5 MiB/s | 288.7 KiB |  00m00s
[ 65/173] Installing libcap-0:2.76-3.fc 100% |  11.6 MiB/s | 512.9 KiB |  00m00s
[ 66/173] Installing systemd-libs-0:258 100% | 118.5 MiB/s |   3.0 MiB |  00m00s
[ 67/173] Installing libsepol-0:3.9-2.f 100% | 104.2 MiB/s |   1.0 MiB |  00m00s
[ 68/173] Installing lz4-libs-0:1.10.0- 100% |  64.0 MiB/s | 262.2 KiB |  00m00s
[ 69/173] Installing json-c-0:0.18-7.fc 100% |  45.5 MiB/s | 139.8 KiB |  00m00s
[ 70/173] Installing alternatives-0:1.3 100% |   2.3 MiB/s |  91.7 KiB |  00m00s
[ 71/173] Installing libffi-0:3.5.2-1.f 100% |  85.2 MiB/s | 349.0 KiB |  00m00s
[ 72/173] Installing p11-kit-0:0.25.8-1 100% |  42.8 MiB/s |   3.0 MiB |  00m00s
[ 73/173] Installing p11-kit-trust-0:0. 100% |  11.4 MiB/s | 595.9 KiB |  00m00s
[ 74/173] Installing pcre2-0:10.47-1.fc 100% | 103.0 MiB/s | 843.4 KiB |  00m00s
[ 75/173] Installing libselinux-0:3.9-5 100% |  65.0 MiB/s | 266.4 KiB |  00m00s
[ 76/173] Installing grep-0:3.12-2.fc43 100% |  19.2 MiB/s |   1.0 MiB |  00m00s
[ 77/173] Installing findutils-1:4.10.0 100% |  34.7 MiB/s |   2.0 MiB |  00m00s
[ 78/173] Installing sed-0:4.9-5.fc43.p 100% |  18.5 MiB/s | 945.3 KiB |  00m00s
[ 79/173] Installing xz-1:5.8.1-4.fc43. 100% |  24.0 MiB/s |   1.4 MiB |  00m00s
[ 80/173] Installing libmount-0:2.41.3- 100% |  89.4 MiB/s | 549.3 KiB |  00m00s
[ 81/173] Installing lua-libs-0:5.4.8-4 100% |  64.3 MiB/s | 395.3 KiB |  00m00s
[ 82/173] Installing util-linux-core-0: 100% |  39.5 MiB/s |   2.5 MiB |  00m00s
[ 83/173] Installing openssl-libs-1:3.5 100% | 125.7 MiB/s |   9.0 MiB |  00m00s
[ 84/173] Installing coreutils-0:9.7-7. 100% |  77.8 MiB/s |   9.4 MiB |  00m00s
[ 85/173] Installing ca-certificates-0: 100% | 665.9 KiB/s |   2.5 MiB |  00m04s
[ 86/173] Installing gzip-0:1.13-4.fc43 100% |   7.5 MiB/s | 430.2 KiB |  00m00s
[ 87/173] Installing libfsverity-0:1.6- 100% |  33.7 MiB/s |  69.1 KiB |  00m00s
[ 88/173] Installing libevent-0:2.1.12- 100% | 110.0 MiB/s |   1.2 MiB |  00m00s
[ 89/173] Installing rpm-sequoia-0:1.10 100% | 126.0 MiB/s |   4.9 MiB |  00m00s
[ 90/173] Installing tar-2:1.35-6.fc43. 100% |  44.1 MiB/s |   3.1 MiB |  00m00s
[ 91/173] Installing libsemanage-0:3.9- 100% |  69.3 MiB/s | 425.7 KiB |  00m00s
[ 92/173] Installing systemd-standalone 100% |   9.6 MiB/s | 394.1 KiB |  00m00s
[ 93/173] Installing rpm-libs-0:6.0.1-1 100% | 102.0 MiB/s |   1.2 MiB |  00m00s
[ 94/173] Installing zstd-0:1.5.7-2.fc4 100% |  36.0 MiB/s |   1.9 MiB |  00m00s
[ 95/173] Installing libusb1-0:1.0.29-4 100% |  14.9 MiB/s | 244.4 KiB |  00m00s
>>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.ppc64le                 
>>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.ppc64le                
>>> Scriptlet output:                                                           
>>> Creating group 'tss' with GID 59.                                           
>>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59.   
>>>                                                                             
[ 96/173] Installing tpm2-tss-0:4.1.3-8 100% | 112.2 MiB/s |   2.5 MiB |  00m00s
[ 97/173] Installing ima-evm-utils-libs 100% |  30.6 MiB/s |  93.9 KiB |  00m00s
[ 98/173] Installing gnupg2-gpg-agent-0 100% |  18.0 MiB/s | 979.0 KiB |  00m00s
[ 99/173] Installing zip-0:3.0-44.fc43. 100% |  19.0 MiB/s | 893.7 KiB |  00m00s
[100/173] Installing gnupg2-keyboxd-0:2 100% |  32.4 MiB/s | 298.5 KiB |  00m00s
[101/173] Installing libpsl-0:0.21.5-6. 100% |  65.1 MiB/s | 133.2 KiB |  00m00s
[102/173] Installing liblastlog2-0:2.41 100% |  17.0 MiB/s | 139.5 KiB |  00m00s
[103/173] Installing libfdisk-0:2.41.3- 100% |  67.5 MiB/s | 484.0 KiB |  00m00s
[104/173] Installing nettle-0:3.10.1-2. 100% |  85.3 MiB/s | 960.9 KiB |  00m00s
[105/173] Installing gnutls-0:3.8.11-5. 100% | 119.8 MiB/s |   4.1 MiB |  00m00s
[106/173] Installing libxml2-0:2.12.10- 100% |  39.8 MiB/s |   2.3 MiB |  00m00s
[107/173] Installing libarchive-0:3.8.4 100% |  97.5 MiB/s |   1.3 MiB |  00m00s
[108/173] Installing bzip2-0:1.0.8-21.f 100% |   4.3 MiB/s | 175.7 KiB |  00m00s
[109/173] Installing add-determinism-0: 100% |  43.0 MiB/s |   2.5 MiB |  00m00s
[110/173] Installing build-reproducibil 100% |   1.0 MiB/s |   1.0 KiB |  00m00s
[111/173] Installing cpio-0:2.15-6.fc43 100% |  22.7 MiB/s |   1.2 MiB |  00m00s
[112/173] Installing diffutils-0:3.12-3 100% |  29.6 MiB/s |   1.7 MiB |  00m00s
[113/173] Installing ed-0:1.22.2-1.fc43 100% |   3.8 MiB/s | 158.2 KiB |  00m00s
[114/173] Installing patch-0:2.8-2.fc43 100% |   6.1 MiB/s | 264.0 KiB |  00m00s
[115/173] Installing librtas-0:2.0.6-4. 100% |  17.7 MiB/s | 307.5 KiB |  00m00s
[116/173] Installing libpkgconf-0:2.3.0 100% |  43.9 MiB/s | 135.0 KiB |  00m00s
[117/173] Installing pkgconf-0:2.3.0-3. 100% |   2.7 MiB/s | 114.8 KiB |  00m00s
[118/173] Installing pkgconf-pkg-config 100% |  45.5 KiB/s |   1.8 KiB |  00m00s
[119/173] Installing jansson-0:2.14-3.f 100% |  51.6 MiB/s | 158.4 KiB |  00m00s
[120/173] Installing gdbm-libs-1:1.23-1 100% |  57.4 MiB/s | 235.2 KiB |  00m00s
[121/173] Installing cyrus-sasl-lib-0:2 100% |  45.6 MiB/s |   2.9 MiB |  00m00s
[122/173] Installing libgomp-0:15.2.1-5 100% |  90.2 MiB/s | 646.6 KiB |  00m00s
[123/173] Installing libtool-ltdl-0:2.5 100% |  30.9 MiB/s |  95.0 KiB |  00m00s
[124/173] Installing openldap-0:2.6.10- 100% |  87.3 MiB/s | 893.7 KiB |  00m00s
[125/173] Installing gnupg2-dirmngr-0:2 100% |  14.9 MiB/s | 840.8 KiB |  00m00s
[126/173] Installing gnupg2-0:2.4.9-4.f 100% |  71.3 MiB/s |   6.9 MiB |  00m00s
[127/173] Installing rpm-sign-libs-0:6. 100% |  22.3 MiB/s |  68.5 KiB |  00m00s
[128/173] Installing gpgverify-0:2.2-3. 100% |   4.6 MiB/s |   9.4 KiB |  00m00s
[129/173] Installing xxhash-libs-0:0.8. 100% |  28.3 MiB/s |  87.0 KiB |  00m00s
[130/173] Installing libnghttp2-0:1.66. 100% |  64.8 MiB/s | 199.0 KiB |  00m00s
[131/173] Installing keyutils-libs-0:1. 100% |  32.4 MiB/s |  99.4 KiB |  00m00s
[132/173] Installing libcom_err-0:1.47. 100% |  54.8 MiB/s | 112.1 KiB |  00m00s
[133/173] Installing libverto-0:0.3.2-1 100% |  23.1 MiB/s |  70.9 KiB |  00m00s
[134/173] Installing krb5-libs-0:1.21.3 100% |  99.0 MiB/s |   3.0 MiB |  00m00s
[135/173] Installing libssh-0:0.11.3-1. 100% |  87.6 MiB/s | 717.3 KiB |  00m00s
[136/173] Installing libbrotli-0:1.2.0- 100% |  92.2 MiB/s |   1.0 MiB |  00m00s
[137/173] Installing libcurl-0:8.15.0-5 100% |  95.4 MiB/s |   1.1 MiB |  00m00s
[138/173] Installing curl-0:8.15.0-5.fc 100% |   8.7 MiB/s | 524.0 KiB |  00m00s
[139/173] Installing rpm-0:6.0.1-1.fc43 100% |  29.0 MiB/s |   2.8 MiB |  00m00s
[140/173] Installing efi-srpm-macros-0: 100% |  13.4 MiB/s |  41.1 KiB |  00m00s
[141/173] Installing java-srpm-macros-0 100% |   1.1 MiB/s |   1.1 KiB |  00m00s
[142/173] Installing lua-srpm-macros-0: 100% |   1.9 MiB/s |   1.9 KiB |  00m00s
[143/173] Installing tree-sitter-srpm-m 100% |   4.5 MiB/s |   9.3 KiB |  00m00s
[144/173] Installing zig-srpm-macros-0: 100% |   1.6 MiB/s |   1.7 KiB |  00m00s
[145/173] Installing filesystem-srpm-ma 100% |  19.0 MiB/s |  38.9 KiB |  00m00s
[146/173] Installing elfutils-default-y 100% | 340.5 KiB/s |   2.0 KiB |  00m00s
[147/173] Installing elfutils-libs-0:0. 100% |  95.1 MiB/s | 876.4 KiB |  00m00s
[148/173] Installing elfutils-debuginfo 100% |   3.4 MiB/s | 145.8 KiB |  00m00s
[149/173] Installing elfutils-0:0.194-1 100% |  51.5 MiB/s |   3.5 MiB |  00m00s
[150/173] Installing binutils-0:2.45.1- 100% | 114.9 MiB/s |  33.1 MiB |  00m00s
[151/173] Installing gdb-minimal-0:17.1 100% | 101.9 MiB/s |  16.1 MiB |  00m00s
[152/173] Installing debugedit-0:5.2-3. 100% |   8.7 MiB/s | 384.8 KiB |  00m00s
[153/173] Installing rpm-build-libs-0:6 100% |  80.3 MiB/s | 328.8 KiB |  00m00s
[154/173] Installing perl-srpm-macros-0 100% |   1.1 MiB/s |   1.1 KiB |  00m00s
[155/173] Installing package-notes-srpm 100% |   2.0 MiB/s |   2.0 KiB |  00m00s
[156/173] Installing openblas-srpm-macr 100% | 382.8 KiB/s | 392.0   B |  00m00s
[157/173] Installing ocaml-srpm-macros- 100% |   2.1 MiB/s |   2.1 KiB |  00m00s
[158/173] Installing kernel-srpm-macros 100% |   2.3 MiB/s |   2.3 KiB |  00m00s
[159/173] Installing ghc-srpm-macros-0: 100% |   1.0 MiB/s |   1.0 KiB |  00m00s
[160/173] Installing gap-srpm-macros-0: 100% |   2.6 MiB/s |   2.7 KiB |  00m00s
[161/173] Installing fpc-srpm-macros-0: 100% | 410.2 KiB/s | 420.0   B |  00m00s
[162/173] Installing ansible-srpm-macro 100% |  17.7 MiB/s |  36.2 KiB |  00m00s
[163/173] Installing rpm-build-0:6.0.1- 100% |  13.7 MiB/s | 672.5 KiB |  00m00s
[164/173] Installing pyproject-srpm-mac 100% |   1.2 MiB/s |   2.5 KiB |  00m00s
[165/173] Installing redhat-rpm-config- 100% |  26.4 MiB/s | 189.1 KiB |  00m00s
[166/173] Installing forge-srpm-macros- 100% |  19.7 MiB/s |  40.3 KiB |  00m00s
[167/173] Installing fonts-srpm-macros- 100% |  27.8 MiB/s |  57.0 KiB |  00m00s
[168/173] Installing go-srpm-macros-0:3 100% |  30.8 MiB/s |  63.0 KiB |  00m00s
[169/173] Installing python-srpm-macros 100% |   8.6 MiB/s |  52.8 KiB |  00m00s
[170/173] Installing util-linux-0:2.41. 100% |  53.3 MiB/s |   7.0 MiB |  00m00s
[171/173] Installing shadow-utils-2:4.1 100% |  44.6 MiB/s |   4.9 MiB |  00m00s
[172/173] Installing which-0:2.23-3.fc4 100% |   3.1 MiB/s | 125.5 KiB |  00m00s
[173/173] Installing info-0:7.2-6.fc43. 100% | 101.9 KiB/s | 485.9 KiB |  00m05s
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: add-determinism-0.6.0-2.fc43.ppc64le
alternatives-1.33-3.fc43.ppc64le
ansible-srpm-macros-1-18.1.fc43.noarch
audit-libs-4.1.2-2.fc43.ppc64le
bash-5.3.0-2.fc43.ppc64le
binutils-2.45.1-4.fc43.ppc64le
build-reproducibility-srpm-macros-0.6.0-2.fc43.noarch
bzip2-1.0.8-21.fc43.ppc64le
bzip2-libs-1.0.8-21.fc43.ppc64le
ca-certificates-2025.2.80_v9.0.304-1.1.fc43.noarch
coreutils-9.7-7.fc43.ppc64le
coreutils-common-9.7-7.fc43.ppc64le
cpio-2.15-6.fc43.ppc64le
crypto-policies-20251125-1.git63291f8.fc43.noarch
curl-8.15.0-5.fc43.ppc64le
cyrus-sasl-lib-2.1.28-33.fc43.ppc64le
debugedit-5.2-3.fc43.ppc64le
diffutils-3.12-3.fc43.ppc64le
dwz-0.16-2.fc43.ppc64le
ed-1.22.2-1.fc43.ppc64le
efi-srpm-macros-6-4.fc43.noarch
elfutils-0.194-1.fc43.ppc64le
elfutils-debuginfod-client-0.194-1.fc43.ppc64le
elfutils-default-yama-scope-0.194-1.fc43.noarch
elfutils-libelf-0.194-1.fc43.ppc64le
elfutils-libs-0.194-1.fc43.ppc64le
fedora-gpg-keys-43-1.noarch
fedora-release-43-25.noarch
fedora-release-common-43-25.noarch
fedora-release-identity-basic-43-25.noarch
fedora-repos-43-1.noarch
file-5.46-8.fc43.ppc64le
file-libs-5.46-8.fc43.ppc64le
filesystem-3.18-50.fc43.ppc64le
filesystem-srpm-macros-3.18-50.fc43.noarch
findutils-4.10.0-6.fc43.ppc64le
fonts-srpm-macros-2.0.5-23.fc43.noarch
forge-srpm-macros-0.4.0-3.fc43.noarch
fpc-srpm-macros-1.3-15.fc43.noarch
gap-srpm-macros-2-1.fc43.noarch
gawk-5.3.2-2.fc43.ppc64le
gdb-minimal-17.1-1.fc43.ppc64le
gdbm-libs-1.23-10.fc43.ppc64le
ghc-srpm-macros-1.9.2-3.fc43.noarch
glibc-2.42-9.fc43.ppc64le
glibc-common-2.42-9.fc43.ppc64le
glibc-gconv-extra-2.42-9.fc43.ppc64le
glibc-minimal-langpack-2.42-9.fc43.ppc64le
gmp-6.3.0-4.fc43.ppc64le
gnat-srpm-macros-7-1.fc43.noarch
gnulib-l10n-20241231-1.fc43.noarch
gnupg2-2.4.9-4.fc43.ppc64le
gnupg2-dirmngr-2.4.9-4.fc43.ppc64le
gnupg2-gpg-agent-2.4.9-4.fc43.ppc64le
gnupg2-gpgconf-2.4.9-4.fc43.ppc64le
gnupg2-keyboxd-2.4.9-4.fc43.ppc64le
gnupg2-verify-2.4.9-4.fc43.ppc64le
gnutls-3.8.11-5.fc43.ppc64le
go-srpm-macros-3.8.0-1.fc43.noarch
gpg-pubkey-c6e7f081cf80e13146676e88829b606631645531-66b6dccf
gpgverify-2.2-3.fc43.noarch
grep-3.12-2.fc43.ppc64le
gzip-1.13-4.fc43.ppc64le
ima-evm-utils-libs-1.6.2-6.fc43.ppc64le
info-7.2-6.fc43.ppc64le
jansson-2.14-3.fc43.ppc64le
java-srpm-macros-1-7.fc43.noarch
json-c-0.18-7.fc43.ppc64le
kernel-srpm-macros-1.0-27.fc43.noarch
keyutils-libs-1.6.3-6.fc43.ppc64le
krb5-libs-1.21.3-7.fc43.ppc64le
libacl-2.3.2-4.fc43.ppc64le
libarchive-3.8.4-1.fc43.ppc64le
libassuan-2.5.7-4.fc43.ppc64le
libattr-2.5.2-6.fc43.ppc64le
libblkid-2.41.3-7.fc43.ppc64le
libbrotli-1.2.0-1.fc43.ppc64le
libcap-2.76-3.fc43.ppc64le
libcap-ng-0.8.5-8.fc43.ppc64le
libcom_err-1.47.3-2.fc43.ppc64le
libcurl-8.15.0-5.fc43.ppc64le
libeconf-0.7.9-2.fc43.ppc64le
libevent-2.1.12-16.fc43.ppc64le
libfdisk-2.41.3-7.fc43.ppc64le
libffi-3.5.2-1.fc43.ppc64le
libfsverity-1.6-3.fc43.ppc64le
libgcc-15.2.1-5.fc43.ppc64le
libgcrypt-1.11.1-3.fc43.ppc64le
libgomp-15.2.1-5.fc43.ppc64le
libgpg-error-1.55-2.fc43.ppc64le
libidn2-2.3.8-2.fc43.ppc64le
libksba-1.6.7-4.fc43.ppc64le
liblastlog2-2.41.3-7.fc43.ppc64le
libmount-2.41.3-7.fc43.ppc64le
libnghttp2-1.66.0-2.fc43.ppc64le
libpkgconf-2.3.0-3.fc43.ppc64le
libpsl-0.21.5-6.fc43.ppc64le
librtas-2.0.6-4.fc43.ppc64le
libselinux-3.9-5.fc43.ppc64le
libsemanage-3.9-4.fc43.ppc64le
libsepol-3.9-2.fc43.ppc64le
libsmartcols-2.41.3-7.fc43.ppc64le
libssh-0.11.3-1.fc43.ppc64le
libssh-config-0.11.3-1.fc43.noarch
libstdc++-15.2.1-5.fc43.ppc64le
libtasn1-4.20.0-2.fc43.ppc64le
libtool-ltdl-2.5.4-8.fc43.ppc64le
libunistring-1.1-10.fc43.ppc64le
libusb1-1.0.29-4.fc43.ppc64le
libuuid-2.41.3-7.fc43.ppc64le
libverto-0.3.2-11.fc43.ppc64le
libxcrypt-4.5.2-1.fc43.ppc64le
libxml2-2.12.10-5.fc43.ppc64le
libzstd-1.5.7-2.fc43.ppc64le
lua-libs-5.4.8-4.fc43.ppc64le
lua-srpm-macros-1-16.fc43.noarch
lz4-libs-1.10.0-3.fc43.ppc64le
mpfr-4.2.2-2.fc43.ppc64le
ncurses-base-6.5-7.20250614.fc43.noarch
ncurses-libs-6.5-7.20250614.fc43.ppc64le
nettle-3.10.1-2.fc43.ppc64le
npth-1.8-3.fc43.ppc64le
ocaml-srpm-macros-11-2.fc43.noarch
openblas-srpm-macros-2-20.fc43.noarch
openldap-2.6.10-4.fc43.ppc64le
openssl-libs-3.5.4-1.fc43.ppc64le
p11-kit-0.25.8-1.fc43.ppc64le
p11-kit-trust-0.25.8-1.fc43.ppc64le
package-notes-srpm-macros-0.5-14.fc43.noarch
pam-libs-1.7.1-4.fc43.ppc64le
patch-2.8-2.fc43.ppc64le
pcre2-10.47-1.fc43.ppc64le
pcre2-syntax-10.47-1.fc43.noarch
perl-srpm-macros-1-60.fc43.noarch
pkgconf-2.3.0-3.fc43.ppc64le
pkgconf-m4-2.3.0-3.fc43.noarch
pkgconf-pkg-config-2.3.0-3.fc43.ppc64le
popt-1.19-9.fc43.ppc64le
publicsuffix-list-dafsa-20260116-1.fc43.noarch
pyproject-srpm-macros-1.18.6-1.fc43.noarch
python-srpm-macros-3.14-5.fc43.noarch
qt5-srpm-macros-5.15.18-1.fc43.noarch
qt6-srpm-macros-6.10.1-1.fc43.noarch
readline-8.3-2.fc43.ppc64le
redhat-rpm-config-343-11.fc43.noarch
rpm-6.0.1-1.fc43.ppc64le
rpm-build-6.0.1-1.fc43.ppc64le
rpm-build-libs-6.0.1-1.fc43.ppc64le
rpm-libs-6.0.1-1.fc43.ppc64le
rpm-sequoia-1.10.0-1.fc43.ppc64le
rpm-sign-libs-6.0.1-1.fc43.ppc64le
rust-srpm-macros-28.4-1.fc43.noarch
sed-4.9-5.fc43.ppc64le
setup-2.15.0-26.fc43.noarch
shadow-utils-4.18.0-3.fc43.ppc64le
sqlite-libs-3.50.2-2.fc43.ppc64le
systemd-libs-258.3-2.fc43.ppc64le
systemd-standalone-sysusers-258.3-2.fc43.ppc64le
tar-1.35-6.fc43.ppc64le
tpm2-tss-4.1.3-8.fc43.ppc64le
tree-sitter-srpm-macros-0.4.2-1.fc43.noarch
unzip-6.0-67.fc43.ppc64le
util-linux-2.41.3-7.fc43.ppc64le
util-linux-core-2.41.3-7.fc43.ppc64le
which-2.23-3.fc43.ppc64le
xxhash-libs-0.8.3-3.fc43.ppc64le
xz-5.8.1-4.fc43.ppc64le
xz-libs-5.8.1-4.fc43.ppc64le
zig-srpm-macros-1-5.fc43.noarch
zip-3.0-44.fc43.ppc64le
zlib-ng-compat-2.3.2-2.fc43.ppc64le
zstd-1.5.7-2.fc43.ppc64le
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/samtools-1.23-1.fc43.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-43-ppc64le-1769509389.082718/root/var/log/dnf5.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-wmtr0gny/samtools/samtools.spec) Config(child) 3 minutes 3 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/samtools-1.23-1.fc43.src.rpm)  Config(fedora-43-ppc64le)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-43-ppc64le-bootstrap-1769509389.082718/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-43-ppc64le-bootstrap-1769509389.082718/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/fedora-43-ppc64le-1769509389.082718/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-6.0.1-1.fc43.ppc64le
  rpm-sequoia-1.10.0-1.fc43.ppc64le
  dnf5-5.2.17.0-2.fc43.ppc64le
  dnf5-plugins-5.2.17.0-2.fc43.ppc64le
Finish: chroot init
Start: build phase for samtools-1.23-1.fc43.src.rpm
Start: build setup for samtools-1.23-1.fc43.src.rpm
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/samtools-1.23-1.fc43.src.rpm
Updating and loading repositories:
 Copr repository                        100% |   5.2 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% |  24.5 KiB/s |   9.2 KiB |  00m00s
 updates                                100% |  19.4 KiB/s |   6.4 KiB |  00m00s
Repositories loaded.
Package                 Arch    Version              Repository      Size
Installing:
 gcc                    ppc64le 15.2.1-5.fc43        updates     97.9 MiB
 htslib-devel           ppc64le 1.23-1.fc43          copr_base  449.9 KiB
 htslib-tools           ppc64le 1.23-1.fc43          copr_base    4.6 MiB
 make                   ppc64le 1:4.4.1-11.fc43      fedora       1.9 MiB
 ncurses-devel          ppc64le 6.5-7.20250614.fc43  fedora     893.4 KiB
 perl-FindBin           noarch  1.54-520.fc43        fedora       6.8 KiB
 perl-Getopt-Long       noarch  1:2.58-520.fc43      fedora     144.5 KiB
 perl-interpreter       ppc64le 4:5.42.0-520.fc43    fedora     174.5 KiB
 perl-lib               ppc64le 0.65-520.fc43        fedora       8.5 KiB
 zlib-ng-compat-devel   ppc64le 2.3.2-2.fc43         updates    107.0 KiB
Installing dependencies:
 annobin-docs           noarch  12.99-1.fc43         fedora      98.9 KiB
 annobin-plugin-gcc     ppc64le 12.99-1.fc43         fedora       1.0 MiB
 cmake-filesystem       ppc64le 3.31.10-3.fc43       updates      0.0   B
 cpp                    ppc64le 15.2.1-5.fc43        updates     34.6 MiB
 gcc-plugin-annobin     ppc64le 15.2.1-5.fc43        updates     68.9 KiB
 glibc-devel            ppc64le 2.42-9.fc43          updates      3.6 MiB
 groff-base             ppc64le 1.23.0-11.fc43       updates      4.5 MiB
 htslib                 ppc64le 1.23-1.fc43          copr_base    1.6 MiB
 kernel-headers         ppc64le 6.18.3-200.fc43      updates      6.7 MiB
 libasan                ppc64le 15.2.1-5.fc43        updates      2.1 MiB
 libatomic              ppc64le 15.2.1-5.fc43        updates     68.2 KiB
 libmpc                 ppc64le 1.3.1-8.fc43         fedora     281.6 KiB
 libubsan               ppc64le 15.2.1-5.fc43        updates    668.6 KiB
 libxcrypt-devel        ppc64le 4.5.2-1.fc43         updates     31.1 KiB
 ncurses                ppc64le 6.5-7.20250614.fc43  fedora     956.9 KiB
 ncurses-c++-libs       ppc64le 6.5-7.20250614.fc43  fedora     265.3 KiB
 perl-AutoLoader        noarch  5.74-520.fc43        fedora      20.6 KiB
 perl-B                 ppc64le 1.89-520.fc43        fedora     545.2 KiB
 perl-Carp              noarch  1.54-520.fc43        fedora      46.6 KiB
 perl-Class-Struct      noarch  0.68-520.fc43        fedora      25.4 KiB
 perl-Data-Dumper       ppc64le 2.191-521.fc43       fedora     135.4 KiB
 perl-Digest            noarch  1.20-520.fc43        fedora      35.3 KiB
 perl-Digest-MD5        ppc64le 2.59-520.fc43        fedora     103.4 KiB
 perl-DynaLoader        ppc64le 1.57-520.fc43        fedora      32.1 KiB
 perl-Encode            ppc64le 4:3.21-520.fc43      fedora       4.8 MiB
 perl-Errno             ppc64le 1.38-520.fc43        fedora       8.4 KiB
 perl-Exporter          noarch  5.79-520.fc43        fedora      54.3 KiB
 perl-Fcntl             ppc64le 1.20-520.fc43        fedora      92.5 KiB
 perl-File-Basename     noarch  2.86-520.fc43        fedora      14.0 KiB
 perl-File-Path         noarch  2.18-520.fc43        fedora      63.5 KiB
 perl-File-Temp         noarch  1:0.231.100-520.fc43 fedora     162.3 KiB
 perl-File-stat         noarch  1.14-520.fc43        fedora      12.5 KiB
 perl-FileHandle        noarch  2.05-520.fc43        fedora       9.4 KiB
 perl-Getopt-Std        noarch  1.14-520.fc43        fedora      11.2 KiB
 perl-HTTP-Tiny         noarch  0.090-521.fc43       fedora     154.4 KiB
 perl-IO                ppc64le 1.55-520.fc43        fedora     191.1 KiB
 perl-IO-Socket-IP      noarch  0.43-521.fc43        fedora     100.3 KiB
 perl-IO-Socket-SSL     noarch  2.095-2.fc43         fedora     714.5 KiB
 perl-IPC-Open3         noarch  1.24-520.fc43        fedora      27.7 KiB
 perl-MIME-Base32       noarch  1.303-24.fc43        fedora      30.7 KiB
 perl-MIME-Base64       ppc64le 3.16-520.fc43        fedora      93.7 KiB
 perl-Net-SSLeay        ppc64le 1.94-11.fc43         fedora       1.5 MiB
 perl-POSIX             ppc64le 2.23-520.fc43        fedora     328.3 KiB
 perl-PathTools         ppc64le 3.94-520.fc43        fedora     223.9 KiB
 perl-Pod-Escapes       noarch  1:1.07-520.fc43      fedora      24.9 KiB
 perl-Pod-Perldoc       noarch  3.28.01-521.fc43     fedora     163.7 KiB
 perl-Pod-Simple        noarch  1:3.47-3.fc43        fedora     565.3 KiB
 perl-Pod-Usage         noarch  4:2.05-520.fc43      fedora      86.3 KiB
 perl-Scalar-List-Utils ppc64le 5:1.70-1.fc43        fedora     152.6 KiB
 perl-SelectSaver       noarch  1.02-520.fc43        fedora       2.2 KiB
 perl-Socket            ppc64le 4:2.040-2.fc43       fedora     143.9 KiB
 perl-Storable          ppc64le 1:3.37-521.fc43      fedora     243.1 KiB
 perl-Symbol            noarch  1.09-520.fc43        fedora       6.8 KiB
 perl-Term-ANSIColor    noarch  5.01-521.fc43        fedora      97.5 KiB
 perl-Term-Cap          noarch  1.18-520.fc43        fedora      29.3 KiB
 perl-Text-ParseWords   noarch  3.31-520.fc43        fedora      13.6 KiB
 perl-Text-Tabs+Wrap    noarch  2024.001-520.fc43    fedora      22.6 KiB
 perl-Time-Local        noarch  2:1.350-520.fc43     fedora      69.0 KiB
 perl-URI               noarch  5.34-2.fc43          updates    268.0 KiB
 perl-base              noarch  2.27-520.fc43        fedora      12.6 KiB
 perl-constant          noarch  1.33-521.fc43        fedora      26.2 KiB
 perl-if                noarch  0.61.000-520.fc43    fedora       5.8 KiB
 perl-libnet            noarch  3.15-521.fc43        fedora     289.4 KiB
 perl-libs              ppc64le 4:5.42.0-520.fc43    fedora      12.3 MiB
 perl-locale            noarch  1.13-520.fc43        fedora       6.1 KiB
 perl-mro               ppc64le 1.29-520.fc43        fedora      81.2 KiB
 perl-overload          noarch  1.40-520.fc43        fedora      71.6 KiB
 perl-overloading       noarch  0.02-520.fc43        fedora       4.9 KiB
 perl-parent            noarch  1:0.244-520.fc43     fedora      10.3 KiB
 perl-podlators         noarch  1:6.0.2-520.fc43     fedora     317.5 KiB
 perl-vars              noarch  1.05-520.fc43        fedora       3.9 KiB

Transaction Summary:
 Installing:        81 packages

Total size of inbound packages is 62 MiB. Need to download 62 MiB.
After this operation, 187 MiB extra will be used (install 187 MiB, remove 0 B).
[ 1/81] perl-FindBin-0:1.54-520.fc43.no 100% | 482.0   B/s |  14.2 KiB |  00m30s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
[ 2/81] perl-Getopt-Long-1:2.58-520.fc4 100% | 731.4 KiB/s |  63.6 KiB |  00m00s
[ 3/81] ncurses-devel-0:6.5-7.20250614. 100% |  19.5 KiB/s | 590.1 KiB |  00m30s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
[ 4/81] make-1:4.4.1-11.fc43.ppc64le    100% |  19.9 KiB/s | 602.2 KiB |  00m30s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
[ 5/81] perl-lib-0:0.65-520.fc43.ppc64l 100% | 181.3 KiB/s |  14.9 KiB |  00m00s
[ 6/81] perl-interpreter-4:5.42.0-520.f 100% |   1.5 MiB/s |  72.4 KiB |  00m00s
[ 7/81] htslib-devel-0:1.23-1.fc43.ppc6 100% | 494.7 KiB/s | 106.8 KiB |  00m00s
[ 8/81] htslib-tools-0:1.23-1.fc43.ppc6 100% |   2.6 MiB/s | 835.8 KiB |  00m00s
[ 9/81] ncurses-c++-libs-0:6.5-7.202506 100% | 924.9 KiB/s |  38.8 KiB |  00m00s
[10/81] perl-Carp-0:1.54-520.fc43.noarc 100% | 638.0 KiB/s |  28.7 KiB |  00m00s
[11/81] perl-Exporter-0:5.79-520.fc43.n 100% |   1.0 MiB/s |  30.9 KiB |  00m00s
[12/81] perl-File-Basename-0:2.86-520.f 100% | 592.0 KiB/s |  17.2 KiB |  00m00s
[13/81] perl-PathTools-0:3.94-520.fc43. 100% |   1.9 MiB/s |  87.7 KiB |  00m00s
[14/81] perl-libs-4:5.42.0-520.fc43.ppc 100% |  21.2 MiB/s |   2.7 MiB |  00m00s
[15/81] perl-Pod-Usage-4:2.05-520.fc43. 100% | 921.3 KiB/s |  40.5 KiB |  00m00s
[16/81] perl-Text-ParseWords-0:3.31-520 100% | 340.6 KiB/s |  16.3 KiB |  00m00s
[17/81] perl-base-0:2.27-520.fc43.noarc 100% | 523.3 KiB/s |  16.2 KiB |  00m00s
[18/81] perl-constant-0:1.33-521.fc43.n 100% | 759.0 KiB/s |  22.8 KiB |  00m00s
[19/81] perl-overload-0:1.40-520.fc43.n 100% |   1.1 MiB/s |  45.6 KiB |  00m00s
[20/81] libmpc-0:1.3.1-8.fc43.ppc64le   100% |   1.0 MiB/s |  96.1 KiB |  00m00s
[21/81] zlib-ng-compat-devel-0:2.3.2-2. 100% | 397.0   B/s |  38.0 KiB |  01m38s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
>>> Curl error (28): Timeout was reached for http://fedora-mirror02.rbc.ru/pub/f
>>> Curl error (28): Timeout was reached for http://dl.fedoraproject.org/pub/fed
[22/81] htslib-0:1.23-1.fc43.ppc64le    100% |   3.5 MiB/s | 657.8 KiB |  00m00s
[23/81] perl-Errno-0:1.38-520.fc43.ppc6 100% | 121.8 KiB/s |  14.9 KiB |  00m00s
[24/81] perl-Scalar-List-Utils-5:1.70-1 100% | 722.0 KiB/s |  77.3 KiB |  00m00s
[25/81] perl-DynaLoader-0:1.57-520.fc43 100% | 576.3 KiB/s |  25.9 KiB |  00m00s
[26/81] perl-Encode-4:3.21-520.fc43.ppc 100% |   7.0 MiB/s |   1.0 MiB |  00m00s
[27/81] perl-Pod-Perldoc-0:3.28.01-521. 100% |   2.0 MiB/s |  84.3 KiB |  00m00s
[28/81] perl-podlators-1:6.0.2-520.fc43 100% |   2.4 MiB/s | 128.3 KiB |  00m00s
[29/81] perl-mro-0:1.29-520.fc43.ppc64l 100% |   1.1 MiB/s |  30.3 KiB |  00m00s
[30/81] perl-overloading-0:0.02-520.fc4 100% | 478.1 KiB/s |  12.9 KiB |  00m00s
[31/81] perl-vars-0:1.05-520.fc43.noarc 100% | 481.0 KiB/s |  13.0 KiB |  00m00s
[32/81] perl-Getopt-Std-0:1.14-520.fc43 100% | 581.7 KiB/s |  15.7 KiB |  00m00s
[33/81] perl-MIME-Base64-0:3.16-520.fc4 100% |   1.1 MiB/s |  30.6 KiB |  00m00s
[34/81] perl-Storable-1:3.37-521.fc43.p 100% |   2.3 MiB/s | 102.1 KiB |  00m00s
[35/81] perl-parent-1:0.244-520.fc43.no 100% | 569.4 KiB/s |  14.8 KiB |  00m00s
[36/81] perl-Fcntl-0:1.20-520.fc43.ppc6 100% |   1.1 MiB/s |  30.1 KiB |  00m00s
[37/81] perl-File-Temp-1:0.231.100-520. 100% |   1.3 MiB/s |  59.0 KiB |  00m00s
[38/81] perl-HTTP-Tiny-0:0.090-521.fc43 100% |   2.0 MiB/s |  56.3 KiB |  00m00s
[39/81] perl-IO-0:1.55-520.fc43.ppc64le 100% |   1.5 MiB/s |  82.6 KiB |  00m00s
[40/81] perl-IPC-Open3-0:1.24-520.fc43. 100% | 886.3 KiB/s |  23.9 KiB |  00m00s
[41/81] perl-Pod-Simple-1:3.47-3.fc43.n 100% |   3.6 MiB/s | 219.9 KiB |  00m00s
[42/81] perl-Symbol-0:1.09-520.fc43.noa 100% | 526.0 KiB/s |  14.2 KiB |  00m00s
[43/81] perl-POSIX-0:2.23-520.fc43.ppc6 100% |   2.6 MiB/s | 117.7 KiB |  00m00s
[44/81] perl-Term-ANSIColor-0:5.01-521. 100% | 970.9 KiB/s |  47.6 KiB |  00m00s
[45/81] perl-Term-Cap-0:1.18-520.fc43.n 100% | 812.3 KiB/s |  21.9 KiB |  00m00s
[46/81] perl-File-Path-0:2.18-520.fc43. 100% | 947.4 KiB/s |  35.1 KiB |  00m00s
[47/81] perl-IO-Socket-SSL-0:2.095-2.fc 100% |   4.8 MiB/s | 231.5 KiB |  00m00s
[48/81] perl-Net-SSLeay-0:1.94-11.fc43. 100% |   4.4 MiB/s | 388.0 KiB |  00m00s
[49/81] perl-Socket-4:2.040-2.fc43.ppc6 100% |   2.0 MiB/s |  55.5 KiB |  00m00s
[50/81] perl-Time-Local-2:1.350-520.fc4 100% |   1.2 MiB/s |  34.4 KiB |  00m00s
[51/81] perl-File-stat-0:1.14-520.fc43. 100% | 632.0 KiB/s |  17.1 KiB |  00m00s
[52/81] perl-SelectSaver-0:1.02-520.fc4 100% | 434.2 KiB/s |  11.7 KiB |  00m00s
[53/81] perl-Pod-Escapes-1:1.07-520.fc4 100% | 732.6 KiB/s |  19.8 KiB |  00m00s
[54/81] perl-Text-Tabs+Wrap-0:2024.001- 100% | 832.1 KiB/s |  21.6 KiB |  00m00s
[55/81] perl-if-0:0.61.000-520.fc43.noa 100% | 437.6 KiB/s |  14.0 KiB |  00m00s
[56/81] perl-locale-0:1.13-520.fc43.noa 100% | 500.1 KiB/s |  13.5 KiB |  00m00s
[57/81] ncurses-0:6.5-7.20250614.fc43.p 100% |   7.3 MiB/s | 435.9 KiB |  00m00s
[58/81] perl-IO-Socket-IP-0:0.43-521.fc 100% |   1.5 MiB/s |  42.1 KiB |  00m00s
[59/81] perl-AutoLoader-0:5.74-520.fc43 100% | 559.1 KiB/s |  21.2 KiB |  00m00s
[60/81] perl-Class-Struct-0:0.68-520.fc 100% | 817.6 KiB/s |  22.1 KiB |  00m00s
[61/81] cmake-filesystem-0:3.31.10-3.fc 100% | 328.3 KiB/s |  13.8 KiB |  00m00s
[62/81] glibc-devel-0:2.42-9.fc43.ppc64 100% |   3.3 MiB/s | 612.6 KiB |  00m00s
[63/81] libasan-0:15.2.1-5.fc43.ppc64le 100% |   5.7 MiB/s | 547.2 KiB |  00m00s
[64/81] libatomic-0:15.2.1-5.fc43.ppc64 100% |   1.2 MiB/s |  47.0 KiB |  00m00s
[65/81] libubsan-0:15.2.1-5.fc43.ppc64l 100% |   3.4 MiB/s | 278.1 KiB |  00m00s
[66/81] groff-base-0:1.23.0-11.fc43.ppc 100% |   9.6 MiB/s |   1.1 MiB |  00m00s
[67/81] perl-URI-0:5.34-2.fc43.noarch   100% |   2.0 MiB/s | 149.3 KiB |  00m00s
[68/81] perl-Data-Dumper-0:2.191-521.fc 100% |   1.2 MiB/s |  58.3 KiB |  00m00s
[69/81] perl-MIME-Base32-0:1.303-24.fc4 100% | 753.8 KiB/s |  20.4 KiB |  00m00s
[70/81] perl-libnet-0:3.15-521.fc43.noa 100% |   2.4 MiB/s | 128.3 KiB |  00m00s
[71/81] perl-B-0:1.89-520.fc43.ppc64le  100% |   2.8 MiB/s | 180.6 KiB |  00m00s
[72/81] perl-Digest-MD5-0:2.59-520.fc43 100% | 609.4 KiB/s |  36.0 KiB |  00m00s
[73/81] perl-FileHandle-0:2.05-520.fc43 100% | 553.6 KiB/s |  15.5 KiB |  00m00s
[74/81] perl-Digest-0:1.20-520.fc43.noa 100% | 918.0 KiB/s |  24.8 KiB |  00m00s
[75/81] kernel-headers-0:6.18.3-200.fc4 100% |  16.5 MiB/s |   1.7 MiB |  00m00s
[76/81] libxcrypt-devel-0:4.5.2-1.fc43. 100% | 830.3 KiB/s |  29.9 KiB |  00m00s
[77/81] annobin-plugin-gcc-0:12.99-1.fc 100% |   9.6 MiB/s | 998.7 KiB |  00m00s
[78/81] gcc-plugin-annobin-0:15.2.1-5.f 100% |   1.7 MiB/s |  62.3 KiB |  00m00s
[79/81] annobin-docs-0:12.99-1.fc43.noa 100% |   1.4 MiB/s |  89.5 KiB |  00m00s
[80/81] cpp-0:15.2.1-5.fc43.ppc64le     100% | 113.8 KiB/s |  11.4 MiB |  01m42s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
>>> Curl error (28): Timeout was reached for http://fedora-mirror02.rbc.ru/pub/f
>>> Curl error (28): Timeout was reached for http://dl.fedoraproject.org/pub/fed
[81/81] gcc-0:15.2.1-5.fc43.ppc64le     100% | 257.8 KiB/s |  34.9 MiB |  02m18s
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
>>> Curl error (28): Timeout was reached for http://fedora-mirror02.rbc.ru/pub/f
>>> Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/fe
>>> Curl error (28): Timeout was reached for http://fedora-mirror02.rbc.ru/pub/f
--------------------------------------------------------------------------------
[81/81] Total                           100% | 375.4 KiB/s |  61.9 MiB |  02m49s
Running transaction
[ 1/83] Verify package files            100% |  86.0   B/s |  81.0   B |  00m01s
[ 2/83] Prepare transaction             100% | 578.0   B/s |  81.0   B |  00m00s
[ 3/83] Installing htslib-0:1.23-1.fc43 100% |  91.8 MiB/s |   1.7 MiB |  00m00s
[ 4/83] Installing libmpc-0:1.3.1-8.fc4 100% |  55.3 MiB/s | 283.1 KiB |  00m00s
[ 5/83] Installing cpp-0:15.2.1-5.fc43. 100% | 110.7 MiB/s |  34.6 MiB |  00m00s
[ 6/83] Installing annobin-docs-0:12.99 100% |  12.2 MiB/s | 100.1 KiB |  00m00s
[ 7/83] Installing kernel-headers-0:6.1 100% |  52.2 MiB/s |   6.9 MiB |  00m00s
[ 8/83] Installing glibc-devel-0:2.42-9 100% |  56.0 MiB/s |   3.7 MiB |  00m00s
[ 9/83] Installing libxcrypt-devel-0:4. 100% |   2.5 MiB/s |  33.4 KiB |  00m00s
[10/83] Installing groff-base-0:1.23.0- 100% |  46.0 MiB/s |   4.5 MiB |  00m00s
[11/83] Installing libubsan-0:15.2.1-5. 100% |  93.4 MiB/s | 669.4 KiB |  00m00s
[12/83] Installing libatomic-0:15.2.1-5 100% |  33.7 MiB/s |  69.0 KiB |  00m00s
[13/83] Installing libasan-0:15.2.1-5.f 100% | 131.5 MiB/s |   2.1 MiB |  00m00s
[14/83] Installing cmake-filesystem-0:3 100% |   1.5 MiB/s |   7.6 KiB |  00m00s
[15/83] Installing ncurses-0:6.5-7.2025 100% |  19.2 MiB/s | 963.5 KiB |  00m00s
[16/83] Installing perl-Digest-0:1.20-5 100% |  12.1 MiB/s |  37.1 KiB |  00m00s
[17/83] Installing perl-Digest-MD5-0:2. 100% |  34.3 MiB/s | 105.3 KiB |  00m00s
[18/83] Installing perl-FileHandle-0:2. 100% |   9.6 MiB/s |   9.8 KiB |  00m00s
[19/83] Installing perl-B-0:1.89-520.fc 100% |  67.0 MiB/s | 548.6 KiB |  00m00s
[20/83] Installing perl-libnet-0:3.15-5 100% |  48.0 MiB/s | 294.7 KiB |  00m00s
[21/83] Installing perl-Data-Dumper-0:2 100% |  44.7 MiB/s | 137.3 KiB |  00m00s
[22/83] Installing perl-MIME-Base32-0:1 100% |  10.5 MiB/s |  32.2 KiB |  00m00s
[23/83] Installing perl-URI-0:5.34-2.fc 100% |  22.9 MiB/s | 281.8 KiB |  00m00s
[24/83] Installing perl-IO-Socket-IP-0: 100% |  33.3 MiB/s | 102.2 KiB |  00m00s
[25/83] Installing perl-AutoLoader-0:5. 100% |  20.5 MiB/s |  21.0 KiB |  00m00s
[26/83] Installing perl-IO-Socket-SSL-0 100% |  78.0 MiB/s | 718.6 KiB |  00m00s
[27/83] Installing perl-Net-SSLeay-0:1. 100% |  74.2 MiB/s |   1.6 MiB |  00m00s
[28/83] Installing perl-locale-0:1.13-5 100% |   6.4 MiB/s |   6.5 KiB |  00m00s
[29/83] Installing perl-if-0:0.61.000-5 100% |   6.1 MiB/s |   6.2 KiB |  00m00s
[30/83] Installing perl-Text-Tabs+Wrap- 100% |  11.7 MiB/s |  23.9 KiB |  00m00s
[31/83] Installing perl-Pod-Escapes-1:1 100% |  12.7 MiB/s |  25.9 KiB |  00m00s
[32/83] Installing perl-Time-Local-2:1. 100% |  34.5 MiB/s |  70.6 KiB |  00m00s
[33/83] Installing perl-File-Path-0:2.1 100% |  31.5 MiB/s |  64.5 KiB |  00m00s
[34/83] Installing perl-Pod-Simple-1:3. 100% |  62.4 MiB/s | 574.9 KiB |  00m00s
[35/83] Installing perl-HTTP-Tiny-0:0.0 100% |  50.9 MiB/s | 156.4 KiB |  00m00s
[36/83] Installing perl-Class-Struct-0: 100% |  25.3 MiB/s |  25.9 KiB |  00m00s
[37/83] Installing perl-IPC-Open3-0:1.2 100% |  13.9 MiB/s |  28.5 KiB |  00m00s
[38/83] Installing perl-File-Temp-1:0.2 100% |  53.4 MiB/s | 164.1 KiB |  00m00s
[39/83] Installing perl-POSIX-0:2.23-52 100% |  80.5 MiB/s | 329.5 KiB |  00m00s
[40/83] Installing perl-Term-Cap-0:1.18 100% |  14.9 MiB/s |  30.6 KiB |  00m00s
[41/83] Installing perl-Term-ANSIColor- 100% |  32.3 MiB/s |  99.2 KiB |  00m00s
[42/83] Installing perl-podlators-1:6.0 100% |   6.7 MiB/s | 321.4 KiB |  00m00s
[43/83] Installing perl-Pod-Perldoc-0:3 100% |   3.8 MiB/s | 169.2 KiB |  00m00s
[44/83] Installing perl-File-stat-0:1.1 100% |  12.8 MiB/s |  13.1 KiB |  00m00s
[45/83] Installing perl-SelectSaver-0:1 100% |   1.3 MiB/s |   2.6 KiB |  00m00s
[46/83] Installing perl-Socket-4:2.040- 100% |  35.6 MiB/s | 145.9 KiB |  00m00s
[47/83] Installing perl-Symbol-0:1.09-5 100% |   7.1 MiB/s |   7.3 KiB |  00m00s
[48/83] Installing perl-Pod-Usage-4:2.0 100% |   2.1 MiB/s |  87.9 KiB |  00m00s
[49/83] Installing perl-IO-0:1.55-520.f 100% |  38.2 MiB/s | 195.4 KiB |  00m00s
[50/83] Installing perl-Fcntl-0:1.20-52 100% |  45.7 MiB/s |  93.6 KiB |  00m00s
[51/83] Installing perl-overloading-0:0 100% |   2.7 MiB/s |   5.6 KiB |  00m00s
[52/83] Installing perl-mro-0:1.29-520. 100% |  40.2 MiB/s |  82.3 KiB |  00m00s
[53/83] Installing perl-base-0:2.27-520 100% |  12.7 MiB/s |  13.0 KiB |  00m00s
[54/83] Installing perl-Text-ParseWords 100% |   7.1 MiB/s |  14.6 KiB |  00m00s
[55/83] Installing perl-Getopt-Long-1:2 100% |  35.9 MiB/s | 147.2 KiB |  00m00s
[56/83] Installing perl-Storable-1:3.37 100% |  59.7 MiB/s | 244.7 KiB |  00m00s
[57/83] Installing perl-parent-1:0.244- 100% |  10.7 MiB/s |  11.0 KiB |  00m00s
[58/83] Installing perl-MIME-Base64-0:3 100% |  31.2 MiB/s |  95.9 KiB |  00m00s
[59/83] Installing perl-Getopt-Std-0:1. 100% |  11.5 MiB/s |  11.8 KiB |  00m00s
[60/83] Installing perl-vars-0:1.05-520 100% |   4.2 MiB/s |   4.3 KiB |  00m00s
[61/83] Installing perl-overload-0:1.40 100% |  35.2 MiB/s |  72.0 KiB |  00m00s
[62/83] Installing perl-Scalar-List-Uti 100% |  30.5 MiB/s | 156.4 KiB |  00m00s
[63/83] Installing perl-Errno-0:1.38-52 100% |   8.6 MiB/s |   8.8 KiB |  00m00s
[64/83] Installing perl-constant-0:1.33 100% |  13.4 MiB/s |  27.4 KiB |  00m00s
[65/83] Installing perl-File-Basename-0 100% |   7.1 MiB/s |  14.6 KiB |  00m00s
[66/83] Installing perl-Encode-4:3.21-5 100% |  59.8 MiB/s |   4.8 MiB |  00m00s
[67/83] Installing perl-DynaLoader-0:1. 100% |  15.9 MiB/s |  32.5 KiB |  00m00s
[68/83] Installing perl-PathTools-0:3.9 100% |  37.2 MiB/s | 228.4 KiB |  00m00s
[69/83] Installing perl-Exporter-0:5.79 100% |  27.1 MiB/s |  55.6 KiB |  00m00s
[70/83] Installing perl-Carp-0:1.54-520 100% |   7.8 MiB/s |  47.7 KiB |  00m00s
[71/83] Installing perl-libs-4:5.42.0-5 100% |  80.2 MiB/s |  12.4 MiB |  00m00s
[72/83] Installing perl-interpreter-4:5 100% |   4.1 MiB/s | 176.2 KiB |  00m00s
[73/83] Installing ncurses-c++-libs-0:6 100% |  65.0 MiB/s | 266.4 KiB |  00m00s
[74/83] Installing make-1:4.4.1-11.fc43 100% |  30.9 MiB/s |   1.9 MiB |  00m00s
[75/83] Installing gcc-0:15.2.1-5.fc43. 100% | 125.5 MiB/s |  97.9 MiB |  00m01s
[76/83] Installing annobin-plugin-gcc-0 100% |  39.9 MiB/s |   1.0 MiB |  00m00s
[77/83] Installing gcc-plugin-annobin-0 100% |   2.5 MiB/s |  70.6 KiB |  00m00s
[78/83] Installing ncurses-devel-0:6.5- 100% |  10.1 MiB/s |   1.0 MiB |  00m00s
[79/83] Installing perl-FindBin-0:1.54- 100% |   7.0 MiB/s |   7.2 KiB |  00m00s
[80/83] Installing perl-lib-0:0.65-520. 100% |   8.7 MiB/s |   8.9 KiB |  00m00s
[81/83] Installing zlib-ng-compat-devel 100% |  35.3 MiB/s | 108.6 KiB |  00m00s
[82/83] Installing htslib-devel-0:1.23- 100% |  74.0 MiB/s | 454.4 KiB |  00m00s
[83/83] Installing htslib-tools-0:1.23- 100% |  12.0 MiB/s |   4.6 MiB |  00m00s
Warning: skipped OpenPGP checks for 3 packages from repository: copr_base
Complete!
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/samtools-1.23-1.fc43.src.rpm
Updating and loading repositories:
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Repositories loaded.
Nothing to do.
Package "gcc-15.2.1-5.fc43.ppc64le" is already installed.
Package "htslib-devel-1.23-1.fc43.ppc64le" is already installed.
Package "htslib-tools-1.23-1.fc43.ppc64le" is already installed.
Package "make-1:4.4.1-11.fc43.ppc64le" is already installed.
Package "ncurses-devel-6.5-7.20250614.fc43.ppc64le" is already installed.
Package "perl-FindBin-1.54-520.fc43.noarch" is already installed.
Package "perl-Getopt-Long-1:2.58-520.fc43.noarch" is already installed.
Package "perl-lib-0.65-520.fc43.ppc64le" is already installed.
Package "perl-interpreter-4:5.42.0-520.fc43.ppc64le" is already installed.
Package "zlib-ng-compat-devel-2.3.2-2.fc43.ppc64le" is already installed.

Finish: build setup for samtools-1.23-1.fc43.src.rpm
Start: rpmbuild samtools-1.23-1.fc43.src.rpm
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1769040000
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.2KRyrx
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.HKZnIy
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-build
+ cd /builddir/build/BUILD/samtools-1.23-build
+ rm -rf samtools-1.23
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/samtools-1.23.tar.bz2
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd samtools-1.23
+ /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.r0Mg6H
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection  '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection  '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules  '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.23
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection  '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection  '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules  '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']'
++ find . -type f -name configure -print
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed -r --in-place=.backup '/lt_cv_sys_global_symbol_to_cdecl=/s#(".*"|'\''.*'\'')#"sed -n -e '\''s/^T .* \\(.*\\)$/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};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup '/lt_cv_sys_global_symbol_to_cdecl=/s#(".*"|'\''.*'\'')#"sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./htslib-1.23/config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./htslib-1.23/config.guess
++ basename ./htslib-1.23/config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./htslib-1.23/config.guess
'/usr/lib/rpm/redhat/config.guess' -> './htslib-1.23/config.guess'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./htslib-1.23/config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./htslib-1.23/config.sub
++ basename ./htslib-1.23/config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./htslib-1.23/config.sub
'/usr/lib/rpm/redhat/config.sub' -> './htslib-1.23/config.sub'
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
++ echo --runstatedir=/run
+ ./configure --build=ppc64le-redhat-linux --host=ppc64le-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/bin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  ' --prefix=/usr --with-htslib=system
checking for gawk... gawk
checking for ppc64le-redhat-linux-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for gcc option to enable large file support... none needed
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... yes
checking for working ncursesw/curses.h... yes
checking for library containing cbreak... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
+ /usr/bin/make -O -j5 V=1 VERBOSE=1
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_aux.o bam_aux.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_index.o bam_index.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_cat.o bam_cat.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_md.o bam_md.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_plbuf.o bam_plbuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_reheader.o bam_reheader.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_fastq.o bam_fastq.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_plcmd.o bam_plcmd.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o sam_view.o sam_view.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_rmdupse.o bam_rmdupse.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_stat.o bam_stat.c
echo '#define SAMTOOLS_VERSION "1.23"' > version.h
echo '#define SAMTOOLS_CC "gcc"' >> version.h
echo '#define SAMTOOLS_CPPFLAGS ""' >> version.h
echo '#define SAMTOOLS_CFLAGS "-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection"' >> version.h
echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  "' >> version.h
echo '#define SAMTOOLS_HTSDIR ""' >> version.h
echo '#define SAMTOOLS_LIBS ""' >> version.h
echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> version.h
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_rmdup.o bam_rmdup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_color.o bam_color.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam2bcf.o bam2bcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o cut_target.o cut_target.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o sample.o sample.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_mate.o bam_mate.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o coverage.o coverage.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o padding.o padding.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bedcov.o bedcov.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam2depth.o bam2depth.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o phase.o phase.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o faidx.o faidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o dict.o dict.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_flags.o bam_flags.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o stats_isize.o stats_isize.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bamshuf.o bamshuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_tview.o bam_tview.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_tview_curses.o bam_tview_curses.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_split.o bam_split.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_quickcheck.o bam_quickcheck.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_tview_html.o bam_tview_html.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_lpileup.o bam_lpileup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o tmp_file.o tmp_file.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_addrprg.o bam_addrprg.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_sort.o bam_sort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o stats.o stats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_import.o bam_import.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_ampliconclip.o bam_ampliconclip.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_samples.o bam_samples.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o consensus_pileup.o consensus_pileup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o reference.o reference.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o amplicon_stats.o amplicon_stats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o reset.o reset.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o cram_size.o cram_size.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_markdup.o bam_markdup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o sam_opts.o sam_opts.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o sam_utils.o sam_utils.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam.o bam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_consensus.o bam_consensus.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_checksum.o bam_checksum.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -DMAQ_LONGREADS -I.  -I./lz4  -c -o misc/maq2sam-long.o misc/maq2sam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o misc/maq2sam-short.o misc/maq2sam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bedidx.o bedidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o misc/md5sum-lite.o misc/md5sum-lite.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o misc/md5fa.o misc/md5fa.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/test.o test/test.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o misc/ace2sam.o misc/ace2sam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o misc/wgsim.o misc/wgsim.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/split/test_count_rg.o test/split/test_count_rg.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o lz4/lz4.o lz4/lz4.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bamtk.o bamtk.c
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/split/test_parse_args.o test/split/test_parse_args.c
gcc -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o misc/maq2sam-long misc/maq2sam-long.o -lz 
gcc -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o misc/maq2sam-short misc/maq2sam-short.o -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o misc/ace2sam misc/ace2sam.o -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o misc/md5fa misc/md5fa.o -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o misc/wgsim misc/wgsim.o -lm -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o test/vcf-miniview test/vcf-miniview.o -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz  -lpthread
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz  -lpthread
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o bam_checksum.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz  -lpthread
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.CQX3cH
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-build
+ '[' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/samtools-1.23-build/BUILDROOT
++ dirname /builddir/build/BUILD/samtools-1.23-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/samtools-1.23-build
+ mkdir /builddir/build/BUILD/samtools-1.23-build/BUILDROOT
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection  '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection  '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules  '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.23
+ /usr/bin/make install DESTDIR=/builddir/build/BUILD/samtools-1.23-build/BUILDROOT 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/man/man1
/usr/bin/install -p samtools /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin
/usr/bin/install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/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/BUILD/samtools-1.23-build/BUILDROOT/usr/bin
/usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/man/man1
++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/ace2sam /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/blast2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/bowtie2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/export2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/fasta-sanitize.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/interpolate_sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/maq2sam-long /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/maq2sam-short /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/md5fa /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/md5sum-lite /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/novo2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/plot-ampliconstats /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/plot-bamstats /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/psl2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/sam2vcf.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/samtools /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/samtools.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/seq_cache_populate.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/soap2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/wgsim /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/wgsim_eval.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/zoom2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/blast2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/bowtie2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/export2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/fasta-sanitize.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/interpolate_sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/novo2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/plot-ampliconstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/plot-bamstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/psl2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/sam2vcf.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/samtools.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/seq_cache_populate.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/soap2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/wgsim_eval.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/zoom2sam.pl
+ /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 1.23-1.fc43 --unique-debug-suffix -1.23-1.fc43.ppc64le --unique-debug-src-base samtools-1.23-1.fc43.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.23-build/samtools-1.23
find-debuginfo: starting
Extracting debug info from 7 files
DWARF-compressing 7 files
sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/samtools-1.23-1.fc43.ppc64le
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j5
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j5 /builddir/build/BUILD/samtools-1.23-build/BUILDROOT
Scanned 16 directories and 148 files,
               processed 43 inodes,
               0 modified (0 replaced + 0 rewritten),
               0 unsupported format, 0 errors
Reading /builddir/build/BUILD/samtools-1.23-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.RhJWBH
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection  '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection  '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules  '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.23
+ ldd samtools
+ grep -E -e '/lib(64)?/libhts\.so\.' -e '/lib64/lp64d/libhts\.so\.'
	libhts.so.3 => /lib64/libhts.so.3 (0x00007fffbd610000)
+ 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-build/samtools-1.23/samtools reference test/reference/mpileup.1.tmp.cram
.. ok

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

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

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

test_reference:
	/builddir/build/BUILD/samtools-1.23-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-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/mxwj0ccQcm/bgzip.dat.gz
.. ok

bgzip -c -b 979200 -s 6 /tmp/mxwj0ccQcm/bgzip.dat.gz
.. ok

bgzip -c -b 652804 -s 6 /tmp/mxwj0ccQcm/bgzip.dat.gz
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/mxwj0ccQcm/faidx.fa 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/mxwj0ccQcm/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/mxwj0ccQcm/faidx.fa 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/mxwj0ccQcm/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/mxwj0ccQcm/faidx.fa 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/mxwj0ccQcm/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/mxwj0ccQcm/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/mxwj0ccQcm/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/mxwj0ccQcm/fqidx.fq 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/mxwj0ccQcm/fqidx.fq.gz 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/mxwj0ccQcm/fqidx.fq 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/mxwj0ccQcm/fqidx.fq.gz 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/mxwj0ccQcm/fqidx.fq 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/mxwj0ccQcm/fqidx.fq.gz 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/mxwj0ccQcm/fqidx.fq 1:99998-100007
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/mxwj0ccQcm/fqidx.fq.gz 1:99998-100007
.. ok

.. ok

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

test_dict:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/mxwj0ccQcm/dict.fa.gz
.. ok

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

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

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view /tmp/mxwj0ccQcm/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view /tmp/mxwj0ccQcm/large_chrom.bam ref2:1-541556283
.. ok

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

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /tmp/mxwj0ccQcm/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /tmp/mxwj0ccQcm/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam.bai /tmp/mxwj0ccQcm/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /tmp/mxwj0ccQcm/test_input_1_b_opt.bam.bai ref2
.. ok

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

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

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

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -c /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.bam /tmp/mxwj0ccQcm/auto_indexed.csi && cat /tmp/mxwj0ccQcm/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.cram /tmp/mxwj0ccQcm/auto_indexed.crai && cat /tmp/mxwj0ccQcm/auto_indexed.crai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -c /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.sam /tmp/mxwj0ccQcm/auto_indexed.csi && cat /tmp/mxwj0ccQcm/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -@ 2 /tmp/mxwj0ccQcm/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -@ 2 /tmp/mxwj0ccQcm/large_chrom.bam ref2:1-541556283
.. ok

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

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /tmp/mxwj0ccQcm/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /tmp/mxwj0ccQcm/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam.bai /tmp/mxwj0ccQcm/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /tmp/mxwj0ccQcm/test_input_1_b_opt.bam.bai ref2
.. ok

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

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

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

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.bam /tmp/mxwj0ccQcm/auto_indexed.csi && cat /tmp/mxwj0ccQcm/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.cram /tmp/mxwj0ccQcm/auto_indexed.crai && cat /tmp/mxwj0ccQcm/auto_indexed.crai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.sam /tmp/mxwj0ccQcm/auto_indexed.csi && cat /tmp/mxwj0ccQcm/auto_indexed.csi
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup -b /tmp/mxwj0ccQcm/mpileup.bam.list -f /tmp/mxwj0ccQcm/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup -b /tmp/mxwj0ccQcm/mpileup.cram.list -f /tmp/mxwj0ccQcm/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup -b /tmp/mxwj0ccQcm/mpileup.bam.urllist -f /tmp/mxwj0ccQcm/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup -b /tmp/mxwj0ccQcm/mpileup.cram.urllist -f /tmp/mxwj0ccQcm/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/mxwj0ccQcm/mpileup.ref.fa.gz -r17:1050-1060 /tmp/mxwj0ccQcm/mpileup.1.bam | grep -v mpileup
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/mxwj0ccQcm/mpileup.ref.fa.gz -r17:1050-1060 /tmp/mxwj0ccQcm/mpileup.1.cram | grep -v mpileup
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup /builddir/build/BUILD/samtools-1.23-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/mxwj0ccQcm/view.001.fogn (SAM input)     .. ok

	50: Count -R /tmp/mxwj0ccQcm/view.001.fogn (SAM input)      .. ok

	51: Filter -R /tmp/mxwj0ccQcm/view.001.fogn (BAM input)     .. ok

	52: Count -R /tmp/mxwj0ccQcm/view.001.fogn (BAM input)      .. ok

	53: Filter -R /tmp/mxwj0ccQcm/view.001.fogn (CRAM input)    .. ok

	54: Count -R /tmp/mxwj0ccQcm/view.001.fogn (CRAM input)     .. ok

	55: Filter -R /tmp/mxwj0ccQcm/view.001.fogn -r grp2 (SAM input).. ok

	56: Count -R /tmp/mxwj0ccQcm/view.001.fogn -r grp2 (SAM input).. ok

	57: Filter -R /tmp/mxwj0ccQcm/view.001.fogn -r grp2 (BAM input).. ok

	58: Count -R /tmp/mxwj0ccQcm/view.001.fogn -r grp2 (BAM input).. ok

	59: Filter -R /tmp/mxwj0ccQcm/view.001.fogn -r grp2 (CRAM input).. ok

	60: Count -R /tmp/mxwj0ccQcm/view.001.fogn -r grp2 (CRAM input).. ok

	61: Filter -r grp2 -R /tmp/mxwj0ccQcm/view.001.fogn (SAM input).. ok

	62: Count -r grp2 -R /tmp/mxwj0ccQcm/view.001.fogn (SAM input).. ok

	63: Filter -r grp2 -R /tmp/mxwj0ccQcm/view.001.fogn (BAM input).. ok

	64: Count -r grp2 -R /tmp/mxwj0ccQcm/view.001.fogn (BAM input).. ok

	65: Filter -r grp2 -R /tmp/mxwj0ccQcm/view.001.fogn (CRAM input).. ok

	66: Count -r grp2 -R /tmp/mxwj0ccQcm/view.001.fogn (CRAM input).. ok

	67: Filter -N /tmp/mxwj0ccQcm/view.001.forn (SAM input)     .. ok

	68: Count -N /tmp/mxwj0ccQcm/view.001.forn (SAM input)      .. ok

	69: Filter -N /tmp/mxwj0ccQcm/view.001.forn (BAM input)     .. ok

	70: Count -N /tmp/mxwj0ccQcm/view.001.forn (BAM input)      .. ok

	71: Filter -N /tmp/mxwj0ccQcm/view.001.forn (CRAM input)    .. ok

	72: Count -N /tmp/mxwj0ccQcm/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/mxwj0ccQcm/view.001.fobc (SAM input)  .. ok

	86: Count -D BC:/tmp/mxwj0ccQcm/view.001.fobc (SAM input)   .. ok

	87: Filter -D BC:/tmp/mxwj0ccQcm/view.001.fobc (BAM input)  .. ok

	88: Count -D BC:/tmp/mxwj0ccQcm/view.001.fobc (BAM input)   .. ok

	89: Filter -D BC:/tmp/mxwj0ccQcm/view.001.fobc (CRAM input) .. ok

	90: Count -D BC:/tmp/mxwj0ccQcm/view.001.fobc (CRAM input)  .. ok

	91: Filter -D BC:/tmp/mxwj0ccQcm/view.001.fobc -d BC:TGCA (SAM input).. ok

	92: Count -D BC:/tmp/mxwj0ccQcm/view.001.fobc -d BC:TGCA (SAM input).. ok

	93: Filter -D BC:/tmp/mxwj0ccQcm/view.001.fobc -d BC:TGCA (BAM input).. ok

	94: Count -D BC:/tmp/mxwj0ccQcm/view.001.fobc -d BC:TGCA (BAM input).. ok

	95: Filter -D BC:/tmp/mxwj0ccQcm/view.001.fobc -d BC:TGCA (CRAM input).. ok

	96: Count -D BC:/tmp/mxwj0ccQcm/view.001.fobc -d BC:TGCA (CRAM input).. ok

	97: Filter -d BC:TGCA -D BC:/tmp/mxwj0ccQcm/view.001.fobc (SAM input).. ok

	98: Count -d BC:TGCA -D BC:/tmp/mxwj0ccQcm/view.001.fobc (SAM input).. ok

	99: Filter -d BC:TGCA -D BC:/tmp/mxwj0ccQcm/view.001.fobc (BAM input).. ok

	100: Count -d BC:TGCA -D BC:/tmp/mxwj0ccQcm/view.001.fobc (BAM input).. ok

	101: Filter -d BC:TGCA -D BC:/tmp/mxwj0ccQcm/view.001.fobc (CRAM input).. ok

	102: Count -d BC:TGCA -D BC:/tmp/mxwj0ccQcm/view.001.fobc (CRAM input).. ok

	103: Filter -D RG:/tmp/mxwj0ccQcm/view.001.fogn (SAM input) .. ok

	104: Count -D RG:/tmp/mxwj0ccQcm/view.001.fogn (SAM input)  .. ok

	105: Filter -D RG:/tmp/mxwj0ccQcm/view.001.fogn (BAM input) .. ok

	106: Count -D RG:/tmp/mxwj0ccQcm/view.001.fogn (BAM input)  .. ok

	107: Filter -D RG:/tmp/mxwj0ccQcm/view.001.fogn (CRAM input).. ok

	108: Count -D RG:/tmp/mxwj0ccQcm/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-build/samtools-1.23/samtools view -o /tmp/mxwj0ccQcm/view.test115.sam -h -d TGCA /tmp/mxwj0ccQcm/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-build/samtools-1.23/samtools view -c -d TGCA /tmp/mxwj0ccQcm/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-build/samtools-1.23/samtools view -o /tmp/mxwj0ccQcm/view.test117.sam -h -d TGCA /tmp/mxwj0ccQcm/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-build/samtools-1.23/samtools view -c -d TGCA /tmp/mxwj0ccQcm/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-build/samtools-1.23/samtools view -o /tmp/mxwj0ccQcm/view.test119.sam -h -d TGCA /tmp/mxwj0ccQcm/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-build/samtools-1.23/samtools view -c -d TGCA /tmp/mxwj0ccQcm/view.test006.cram --no-PG


.. expected failure

	121: Filter -D BClong:/tmp/mxwj0ccQcm/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mxwj0ccQcm/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -o /tmp/mxwj0ccQcm/view.test121.sam -h -D BClong:/tmp/mxwj0ccQcm/view.001.fobc /tmp/mxwj0ccQcm/view.001.sam --no-PG


.. expected failure

	122: Count -D BClong:/tmp/mxwj0ccQcm/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mxwj0ccQcm/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -c -D BClong:/tmp/mxwj0ccQcm/view.001.fobc /tmp/mxwj0ccQcm/view.001.sam --no-PG


.. expected failure

	123: Filter -D BClong:/tmp/mxwj0ccQcm/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mxwj0ccQcm/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -o /tmp/mxwj0ccQcm/view.test123.sam -h -D BClong:/tmp/mxwj0ccQcm/view.001.fobc /tmp/mxwj0ccQcm/view.test001.bam --no-PG


.. expected failure

	124: Count -D BClong:/tmp/mxwj0ccQcm/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mxwj0ccQcm/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -c -D BClong:/tmp/mxwj0ccQcm/view.001.fobc /tmp/mxwj0ccQcm/view.test001.bam --no-PG


.. expected failure

	125: Filter -D BClong:/tmp/mxwj0ccQcm/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mxwj0ccQcm/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -o /tmp/mxwj0ccQcm/view.test125.sam -h -D BClong:/tmp/mxwj0ccQcm/view.001.fobc /tmp/mxwj0ccQcm/view.test006.cram --no-PG


.. expected failure

	126: Count -D BClong:/tmp/mxwj0ccQcm/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mxwj0ccQcm/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -c -D BClong:/tmp/mxwj0ccQcm/view.001.fobc /tmp/mxwj0ccQcm/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-build/samtools-1.23/samtools view -o /tmp/mxwj0ccQcm/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/mxwj0ccQcm/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-build/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/mxwj0ccQcm/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-build/samtools-1.23/samtools view -o /tmp/mxwj0ccQcm/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/mxwj0ccQcm/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-build/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/mxwj0ccQcm/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-build/samtools-1.23/samtools view -o /tmp/mxwj0ccQcm/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/mxwj0ccQcm/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-build/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/mxwj0ccQcm/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-build/samtools-1.23/test/dat/view.002.01.bed  (BAM input).. ok

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

test_head:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools head -h 5 -n 5 < /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected  | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/0.fq
.. ok

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

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

test_import:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools fastq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools fastq -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools fastq -N -T RG,BC,QT -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools fastq -N -T RG,BC,QT,MD,ia -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq
.. ok

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -N -s /tmp/mxwj0ccQcm/bam2fq.discard.s.fq -0 /tmp/mxwj0ccQcm/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -N -s /tmp/mxwj0ccQcm/bam2fq.discard.s.fq -0 /tmp/mxwj0ccQcm/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/1_map_cigar.sam | tail -n+4
.. ok

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -s 1 -O sam -b /tmp/dlzIxsKw7X - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam
.. ok

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

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

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

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

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

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/mxwj0ccQcm/merge.tag.1.bam /tmp/mxwj0ccQcm/merge.tag.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/mxwj0ccQcm/merge.tag.3.bam /tmp/mxwj0ccQcm/merge.tag.4.bam
.. ok

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

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/merge/merge.bed - /tmp/mxwj0ccQcm/merge.bed.1.bam /tmp/mxwj0ccQcm/merge.bed.2.bam
.. ok

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

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

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

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

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

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

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

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

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

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

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/mxwj0ccQcm/merge.tag.1.bam /tmp/mxwj0ccQcm/merge.tag.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/mxwj0ccQcm/merge.tag.3.bam /tmp/mxwj0ccQcm/merge.tag.4.bam
.. ok

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

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/merge/merge.bed - /tmp/mxwj0ccQcm/merge.bed.1.bam /tmp/mxwj0ccQcm/merge.bed.2.bam
.. ok

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

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

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /tmp/mxwj0ccQcm/sortout
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /tmp/mxwj0ccQcm/sortout.bam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /tmp/mxwj0ccQcm/sorttmp
.. ok

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

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

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

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

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

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

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

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

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

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

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

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

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /tmp/mxwj0ccQcm/sortout
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /tmp/mxwj0ccQcm/sortout.bam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /tmp/mxwj0ccQcm/sorttmp
.. ok

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/5_markdup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -O sam -r --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/6_remove_dups.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/7_mark_supp_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/12_optical_chain_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/13_optical_barcode_tag.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/14_optical_barcode_name.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/15_optical_barcode_rgx_name.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/17_read_group.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/18_primary_duplicate_count.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/5_markdup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -O sam -r --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/6_remove_dups.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/7_mark_supp_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/12_optical_chain_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/13_optical_barcode_tag.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/14_optical_barcode_name.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/15_optical_barcode_rgx_name.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/17_read_group.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/markdup/18_primary_duplicate_count.sam -
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools bedcov /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools bedcov -j /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools bedcov -g512 -G2048 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools bedcov -c /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov.bam
.. ok

.. ok

.. ok

.. ok

.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -p 5 -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -d RG -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -d an -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -d an -M 3 -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -d nn -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.unk.sam  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split_d_nn.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split_d_nn.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort  -t nn /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split_d_nn.sam |
                /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam - 
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -p 5 -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -d RG -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -d an -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -d an -M 3 -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -d nn -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.unk.sam  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split_d_nn.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split_d_nn.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort  -@ 2 -t nn /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split_d_nn.sam |
                /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam - 
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG /tmp/mxwj0ccQcm/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG /tmp/mxwj0ccQcm/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/test.bed /tmp/mxwj0ccQcm/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -O sam --no-PG -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/longref_name.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -O sam --no-PG - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/longref.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/longref2.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools depth /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/longref.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools depth -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/longref.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/mxwj0ccQcm/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort    -O sam --no-PG -n -m 10M test/large_pos/longref3.sam |
                     /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -O sam --no-PG - - |
                     /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort    -O sam --no-PG -m 10M
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG  --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG  --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/2_both_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/3_multi_ref_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test2.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/4_total_hc_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG  --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG  --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/2_both_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/3_multi_ref_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test2.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/4_total_hc_data.sam
.. ok

test_ampliconstats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_hard_clipped.expected.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_soft_clipped.expected.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_soft_clipped_strand.expected.sam /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset --dupflag | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag < /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view
.. ok

test_reset:
	cat /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.cram
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools reset  --dupflag --reject-PG sam_to_fixed_bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam -e"@PG"
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam --no-RG -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-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-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/seq.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/seq.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -a /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -qv /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -qv -a /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -m /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -m /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 -a /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 -qv /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 -qv -a /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 -m /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 -m /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools coverage /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sample.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools coverage --min-depth 1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sample.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools coverage --min-depth 2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sample.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools coverage --min-depth 2 -Q 8 -q 45 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sample.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools coverage --min-depth 1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sample.sam /tmp/mxwj0ccQcm/sample1.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools coverage --min-depth 4 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sample.sam /tmp/mxwj0ccQcm/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.fc43.ppc64le
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.T8QnXJ
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-build
+ cd samtools-1.23
+ DOCDIR=/builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/doc/samtools
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/AUTHORS /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/ChangeLog.old /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/NEWS.md /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/examples /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/doc/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.WO6C2l
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-build
+ cd samtools-1.23
+ LICENSEDIR=/builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/licenses/samtools
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/licenses/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/LICENSE /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/licenses/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: samtools = 1.23-1.fc43 samtools(ppc-64) = 1.23-1.fc43
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl ld64.so.2()(64bit) ld64.so.2(GLIBC_2.23)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.1)(64bit) libhts.so.3(HTSLIB_1.10)(64bit) libhts.so.3(HTSLIB_1.11)(64bit) libhts.so.3(HTSLIB_1.12)(64bit) libhts.so.3(HTSLIB_1.14)(64bit) libhts.so.3(HTSLIB_1.15)(64bit) libhts.so.3(HTSLIB_1.16)(64bit) libhts.so.3(HTSLIB_1.17)(64bit) libhts.so.3(HTSLIB_1.18)(64bit) libhts.so.3(HTSLIB_1.2.1)(64bit) libhts.so.3(HTSLIB_1.21)(64bit) libhts.so.3(HTSLIB_1.22)(64bit) libhts.so.3(HTSLIB_1.23)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) libhts.so.3(HTSLIB_1.9)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: samtools-debugsource-1.23-1.fc43.ppc64le
Provides: samtools-debugsource = 1.23-1.fc43 samtools-debugsource(ppc-64) = 1.23-1.fc43
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.fc43.ppc64le
Provides: debuginfo(build-id) = 293415aeeffde07cc032492aadbdd1bd58d2f453 debuginfo(build-id) = 2f85847490e176ac2e29140a5aa00f1f7100cd11 debuginfo(build-id) = 53043c921baae54bbe9492ce1ceb459d9cdd9233 debuginfo(build-id) = 9653a86ae7fd7913fcbd8efd0e810588298adf94 debuginfo(build-id) = 96a18617119ad60791d266d9c6eec0ad6ab13ed5 debuginfo(build-id) = b7f36291ee2a1511ef43f2569dc1789b017116ad debuginfo(build-id) = d8fb72d0919b8bf835885b927b960d77d4026170 samtools-debuginfo = 1.23-1.fc43 samtools-debuginfo(ppc-64) = 1.23-1.fc43
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: samtools-debugsource(ppc-64) = 1.23-1.fc43
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/samtools-1.23-build/BUILDROOT
Wrote: /builddir/build/RPMS/samtools-1.23-1.fc43.ppc64le.rpm
Wrote: /builddir/build/RPMS/samtools-debugsource-1.23-1.fc43.ppc64le.rpm
Wrote: /builddir/build/RPMS/samtools-debuginfo-1.23-1.fc43.ppc64le.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.AvwKZ1
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-build
+ test -d /builddir/build/BUILD/samtools-1.23-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/samtools-1.23-build
+ rm -rf /builddir/build/BUILD/samtools-1.23-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild samtools-1.23-1.fc43.src.rpm
Finish: build phase for samtools-1.23-1.fc43.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-43-ppc64le-1769509389.082718/root/var/log/dnf5.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.fc43.src.rpm) Config(child) 4 minutes 37 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "samtools",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc43",
            "arch": "src"
        },
        {
            "name": "samtools",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc43",
            "arch": "ppc64le"
        },
        {
            "name": "samtools-debuginfo",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc43",
            "arch": "ppc64le"
        },
        {
            "name": "samtools-debugsource",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc43",
            "arch": "ppc64le"
        }
    ]
}
RPMResults finished