Warning: Permanently added '2620:52:6:1161:dead:beef:cafe:c114' (ED25519) to the list of known hosts. rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading samtools-1.23.tar.bz2 INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o samtools-1.23.tar.bz2 --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/ron/staging/samtools/samtools-1.23.tar.bz2/md5/7ce93103e5a3796c0009f879853837bb/samtools-1.23.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 9138k 100 9138k 0 0 21.2M 0 --:--:-- --:--:-- --:--:-- 21.3M INFO: Reading stdout from command: md5sum samtools-1.23.tar.bz2 Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-rl974j4p/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-rl974j4p/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769509438.093451 -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-rl974j4p/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-rl974j4p/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769509438.093451 -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-rl974j4p/samtools/samtools.spec) Config(rhel+epel-9-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/rhel+epel-9-ppc64le-bootstrap-1769509438.093451/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using container image: registry.access.redhat.com/ubi9/ubi INFO: Pulling image: registry.access.redhat.com/ubi9/ubi INFO: Tagging container image as mock-bootstrap-1aa850ed-577a-4d4c-8eff-8245d36062a8 INFO: Checking that bcd7d46e5c0dd1b6fd6f9b44ecfafe2c5f49c1cd180c5fb4b4332203269b1697 image matches host's architecture INFO: Copy content of container bcd7d46e5c0dd1b6fd6f9b44ecfafe2c5f49c1cd180c5fb4b4332203269b1697 to /var/lib/mock/rhel+epel-9-ppc64le-bootstrap-1769509438.093451/root INFO: mounting bcd7d46e5c0dd1b6fd6f9b44ecfafe2c5f49c1cd180c5fb4b4332203269b1697 with podman image mount INFO: image bcd7d46e5c0dd1b6fd6f9b44ecfafe2c5f49c1cd180c5fb4b4332203269b1697 as /var/lib/containers/storage/overlay/69fd9b0c33d7673e83121827a635d8fc1b00df4355c4052ef06db4d71387d1f4/merged INFO: umounting image bcd7d46e5c0dd1b6fd6f9b44ecfafe2c5f49c1cd180c5fb4b4332203269b1697 (/var/lib/containers/storage/overlay/69fd9b0c33d7673e83121827a635d8fc1b00df4355c4052ef06db4d71387d1f4/merged) with podman image umount INFO: Removing image mock-bootstrap-1aa850ed-577a-4d4c-8eff-8245d36062a8 INFO: Package manager dnf4 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-ppc64le-1769509438.093451/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf4 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.16.1.3-39.el9.ppc64le python3-dnf-4.14.0-31.el9.noarch python3-dnf-plugins-core-4.3.0-24.el9_7.noarch yum-4.14.0-31.el9.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 11 kB/s | 4.8 kB 00:00 Red Hat Enterprise Linux - BaseOS 52 MB/s | 59 MB 00:01 Red Hat Enterprise Linux - AppStream 60 MB/s | 71 MB 00:01 Red Hat Enterprise Linux - CodeReady Linux Buil 21 MB/s | 13 MB 00:00 Extra Packages for Enterprise Linux 9 - ppc64le 341 kB/s | 20 MB 00:59 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: bash ppc64le 5.1.8-9.el9 baseos 1.7 M bzip2 ppc64le 1.0.8-10.el9_5 baseos 60 k coreutils ppc64le 8.32-39.el9 baseos 1.2 M cpio ppc64le 2.13-16.el9 baseos 286 k diffutils ppc64le 3.7-12.el9 baseos 417 k epel-rpm-macros noarch 9-17.el9 epel 15 k findutils ppc64le 1:4.8.0-7.el9 baseos 589 k gawk ppc64le 5.1.0-6.el9 baseos 1.0 M glibc-minimal-langpack ppc64le 2.34-231.el9_7.2 baseos 22 k grep ppc64le 3.6-5.el9 baseos 281 k gzip ppc64le 1.12-1.el9 baseos 172 k info ppc64le 6.7-15.el9 baseos 256 k patch ppc64le 2.7.6-16.el9 appstream 140 k redhat-release ppc64le 9.7-0.7.el9 baseos 53 k redhat-rpm-config noarch 210-1.el9 appstream 70 k rpm-build ppc64le 4.16.1.3-39.el9 appstream 67 k sed ppc64le 4.8-9.el9 baseos 315 k tar ppc64le 2:1.34-9.el9_7 baseos 916 k unzip ppc64le 6.0-59.el9 baseos 186 k util-linux ppc64le 2.37.4-21.el9 baseos 2.3 M which ppc64le 2.21-30.el9_6 baseos 42 k xz ppc64le 5.2.5-8.el9_0 baseos 238 k Installing dependencies: alternatives ppc64le 1.24-2.el9 baseos 43 k ansible-srpm-macros noarch 1-16.el9 epel 21 k audit-libs ppc64le 3.1.5-7.el9 baseos 137 k basesystem noarch 11-13.el9 baseos 8.0 k binutils ppc64le 2.35.2-67.el9_7.1 baseos 5.0 M binutils-gold ppc64le 2.35.2-67.el9_7.1 baseos 1.0 M bzip2-libs ppc64le 1.0.8-10.el9_5 baseos 46 k ca-certificates noarch 2025.2.80_v9.0.305-91.el9 baseos 1.0 M coreutils-common ppc64le 8.32-39.el9 baseos 2.0 M cracklib ppc64le 2.9.6-27.el9 baseos 100 k cracklib-dicts ppc64le 2.9.6-27.el9 baseos 3.6 M crypto-policies noarch 20250905-1.git377cc42.el9_7 baseos 90 k curl ppc64le 7.76.1-34.el9 baseos 295 k cyrus-sasl-lib ppc64le 2.1.27-22.el9 baseos 856 k debugedit ppc64le 5.0-11.el9 appstream 81 k dwz ppc64le 0.16-1.el9 appstream 140 k ed ppc64le 1.14.2-12.el9 baseos 81 k efi-srpm-macros noarch 6-4.el9 appstream 21 k elfutils ppc64le 0.193-1.el9 baseos 601 k elfutils-debuginfod-client ppc64le 0.193-1.el9 baseos 46 k elfutils-default-yama-scope noarch 0.193-1.el9 baseos 9.7 k elfutils-libelf ppc64le 0.193-1.el9 baseos 211 k elfutils-libs ppc64le 0.193-1.el9 baseos 305 k file ppc64le 5.39-16.el9 baseos 52 k file-libs ppc64le 5.39-16.el9 baseos 604 k filesystem ppc64le 3.16-5.el9 baseos 4.8 M fonts-srpm-macros noarch 1:2.0.5-7.el9.1 appstream 29 k forge-srpm-macros noarch 0.4.0-1.el9 epel 19 k fpc-srpm-macros noarch 1.3-7.el9 epel 7.5 k gdb-minimal ppc64le 16.3-2.el9 appstream 4.6 M gdbm-libs ppc64le 1:1.23-1.el9 baseos 64 k ghc-srpm-macros noarch 1.5.0-6.el9 appstream 9.0 k ghc-srpm-macros-epel noarch 1.9.1-1.el9 epel 7.5 k glibc ppc64le 2.34-231.el9_7.2 baseos 2.7 M glibc-common ppc64le 2.34-231.el9_7.2 baseos 323 k glibc-gconv-extra ppc64le 2.34-231.el9_7.2 baseos 1.7 M gmp ppc64le 1:6.2.0-13.el9 baseos 305 k go-srpm-macros noarch 3.6.0-12.el9_7 appstream 27 k go-srpm-macros-epel noarch 3.8.0-1.el9 epel 26 k groff-base ppc64le 1.22.4-10.el9 baseos 1.1 M json-c ppc64le 0.14-11.el9 baseos 48 k kernel-srpm-macros noarch 1.0-14.el9 appstream 14 k keyutils-libs ppc64le 1.6.3-1.el9 baseos 35 k krb5-libs ppc64le 1.21.1-8.el9_6 baseos 846 k libacl ppc64le 2.3.1-4.el9 baseos 26 k libarchive ppc64le 3.5.3-6.el9_6 baseos 454 k libattr ppc64le 2.5.1-3.el9 baseos 21 k libblkid ppc64le 2.37.4-21.el9 baseos 125 k libbrotli ppc64le 1.0.9-7.el9_5 baseos 339 k libcap ppc64le 2.48-10.el9 baseos 74 k libcap-ng ppc64le 0.8.2-7.el9 baseos 37 k libcom_err ppc64le 1.46.5-8.el9 baseos 27 k libcurl ppc64le 7.76.1-34.el9 baseos 314 k libdb ppc64le 5.3.28-57.el9_6 baseos 817 k libeconf ppc64le 0.4.1-4.el9 baseos 32 k libevent ppc64le 2.1.12-8.el9_4 baseos 281 k libfdisk ppc64le 2.37.4-21.el9 baseos 170 k libffi ppc64le 3.4.2-8.el9 baseos 40 k libgcc ppc64le 11.5.0-11.el9 baseos 74 k libgcrypt ppc64le 1.10.0-11.el9 baseos 599 k libgomp ppc64le 11.5.0-11.el9 baseos 269 k libgpg-error ppc64le 1.42-5.el9 baseos 229 k libidn2 ppc64le 2.3.0-7.el9 baseos 108 k libmount ppc64le 2.37.4-21.el9 baseos 153 k libnghttp2 ppc64le 1.43.0-6.el9 baseos 84 k libpkgconf ppc64le 1.7.3-10.el9 baseos 42 k libpsl ppc64le 0.21.1-5.el9 baseos 68 k libpwquality ppc64le 1.4.4-8.el9 baseos 125 k librtas ppc64le 2.0.6-1.el9 baseos 84 k libselinux ppc64le 3.6-3.el9 baseos 100 k libsemanage ppc64le 3.6-5.el9_6 baseos 133 k libsepol ppc64le 3.6-3.el9 baseos 366 k libsigsegv ppc64le 2.13-4.el9 baseos 31 k libsmartcols ppc64le 2.37.4-21.el9 baseos 70 k libssh ppc64le 0.10.4-17.el9_7 baseos 238 k libssh-config noarch 0.10.4-17.el9_7 baseos 8.1 k libstdc++ ppc64le 11.5.0-11.el9 baseos 837 k libtasn1 ppc64le 4.16.0-9.el9 baseos 82 k libtool-ltdl ppc64le 2.4.6-46.el9 baseos 41 k libunistring ppc64le 0.9.10-15.el9 baseos 507 k libutempter ppc64le 1.2.1-6.el9 baseos 30 k libuuid ppc64le 2.37.4-21.el9 baseos 32 k libverto ppc64le 0.3.2-3.el9 baseos 25 k libxcrypt ppc64le 4.4.18-3.el9 baseos 133 k libxml2 ppc64le 2.9.13-14.el9_7 baseos 823 k libzstd ppc64le 1.5.5-1.el9 baseos 322 k lua-libs ppc64le 5.4.4-4.el9 baseos 149 k lua-srpm-macros noarch 1-6.el9 appstream 10 k lz4-libs ppc64le 1.9.3-5.el9 baseos 88 k mpfr ppc64le 4.1.0-7.el9 baseos 324 k ncurses ppc64le 6.2-12.20210508.el9 baseos 413 k ncurses-base noarch 6.2-12.20210508.el9 baseos 96 k ncurses-libs ppc64le 6.2-12.20210508.el9 baseos 370 k ocaml-srpm-macros noarch 6-6.el9 appstream 9.1 k openblas-srpm-macros noarch 2-11.el9 appstream 8.6 k openldap ppc64le 2.6.8-4.el9 baseos 322 k openssl ppc64le 1:3.5.1-5.el9_7 baseos 1.5 M openssl-fips-provider ppc64le 3.0.7-8.el9 baseos 9.2 k openssl-fips-provider-so ppc64le 3.0.7-8.el9 baseos 563 k openssl-libs ppc64le 1:3.5.1-5.el9_7 baseos 2.4 M p11-kit ppc64le 0.25.3-3.el9_5 baseos 535 k p11-kit-trust ppc64le 0.25.3-3.el9_5 baseos 157 k pam ppc64le 1.5.1-26.el9_6 baseos 662 k pcre ppc64le 8.44-4.el9 baseos 203 k pcre2 ppc64le 10.40-6.el9 baseos 237 k pcre2-syntax noarch 10.40-6.el9 baseos 144 k perl-AutoLoader noarch 5.74-481.1.el9_6 appstream 21 k perl-B ppc64le 1.80-481.1.el9_6 appstream 183 k perl-Carp noarch 1.50-460.el9 appstream 31 k perl-Class-Struct noarch 0.66-481.1.el9_6 appstream 22 k perl-Data-Dumper ppc64le 2.174-462.el9 appstream 59 k perl-Digest noarch 1.19-4.el9 appstream 29 k perl-Digest-MD5 ppc64le 2.58-4.el9 appstream 40 k perl-Encode ppc64le 4:3.08-462.el9 appstream 1.7 M perl-Errno ppc64le 1.30-481.1.el9_6 appstream 14 k perl-Exporter noarch 5.74-461.el9 appstream 34 k perl-Fcntl ppc64le 1.13-481.1.el9_6 appstream 20 k perl-File-Basename noarch 2.85-481.1.el9_6 appstream 17 k perl-File-Path noarch 2.18-4.el9 appstream 38 k perl-File-Temp noarch 1:0.231.100-4.el9 appstream 63 k perl-File-stat noarch 1.09-481.1.el9_6 appstream 17 k perl-FileHandle noarch 2.03-481.1.el9_6 appstream 15 k perl-Getopt-Long noarch 1:2.52-4.el9 appstream 64 k perl-Getopt-Std noarch 1.12-481.1.el9_6 appstream 15 k perl-HTTP-Tiny noarch 0.076-462.el9 appstream 57 k perl-IO ppc64le 1.43-481.1.el9_6 appstream 89 k perl-IO-Socket-IP noarch 0.41-5.el9 appstream 45 k perl-IO-Socket-SSL noarch 2.073-2.el9 appstream 221 k perl-IPC-Open3 noarch 1.21-481.1.el9_6 appstream 22 k perl-MIME-Base64 ppc64le 3.16-4.el9 appstream 35 k perl-Mozilla-CA noarch 20200520-6.el9 appstream 14 k perl-Net-SSLeay ppc64le 1.94-3.el9 appstream 423 k perl-POSIX ppc64le 1.94-481.1.el9_6 appstream 98 k perl-PathTools ppc64le 3.78-461.el9 appstream 93 k perl-Pod-Escapes noarch 1:1.07-460.el9 appstream 22 k perl-Pod-Perldoc noarch 3.28.01-461.el9 appstream 92 k perl-Pod-Simple noarch 1:3.42-4.el9 appstream 229 k perl-Pod-Usage noarch 4:2.01-4.el9 appstream 43 k perl-Scalar-List-Utils ppc64le 4:1.56-462.el9 appstream 78 k perl-SelectSaver noarch 1.02-481.1.el9_6 appstream 11 k perl-Socket ppc64le 4:2.031-4.el9 appstream 59 k perl-Storable ppc64le 1:3.21-460.el9 appstream 101 k perl-Symbol noarch 1.08-481.1.el9_6 appstream 14 k perl-Term-ANSIColor noarch 5.01-461.el9 appstream 51 k perl-Term-Cap noarch 1.17-460.el9 appstream 24 k perl-Text-ParseWords noarch 3.30-460.el9 appstream 18 k perl-Text-Tabs+Wrap noarch 2013.0523-460.el9 appstream 25 k perl-Time-Local noarch 2:1.300-7.el9 appstream 37 k perl-URI noarch 5.09-3.el9 appstream 125 k perl-base noarch 2.27-481.1.el9_6 appstream 16 k perl-constant noarch 1.33-461.el9 appstream 25 k perl-if noarch 0.60.800-481.1.el9_6 appstream 14 k perl-interpreter ppc64le 4:5.32.1-481.1.el9_6 appstream 70 k perl-libnet noarch 3.13-4.el9 appstream 134 k perl-libs ppc64le 4:5.32.1-481.1.el9_6 appstream 2.3 M perl-mro ppc64le 1.23-481.1.el9_6 appstream 28 k perl-overload noarch 1.31-481.1.el9_6 appstream 45 k perl-overloading noarch 0.02-481.1.el9_6 appstream 12 k perl-parent noarch 1:0.238-460.el9 appstream 16 k perl-podlators noarch 1:4.14-460.el9 appstream 118 k perl-srpm-macros noarch 1-41.el9 appstream 9.4 k perl-subs noarch 1.03-481.1.el9_6 appstream 11 k perl-vars noarch 1.05-481.1.el9_6 appstream 13 k pkgconf ppc64le 1.7.3-10.el9 baseos 45 k pkgconf-m4 noarch 1.7.3-10.el9 baseos 16 k pkgconf-pkg-config ppc64le 1.7.3-10.el9 baseos 12 k popt ppc64le 1.18-8.el9 baseos 73 k publicsuffix-list-dafsa noarch 20210518-3.el9 baseos 59 k pyproject-srpm-macros noarch 1.16.2-1.el9 appstream 14 k python-srpm-macros noarch 3.9-54.el9 appstream 18 k qt5-srpm-macros noarch 5.15.9-1.el9 appstream 9.1 k qt6-srpm-macros noarch 6.6.2-1.el9 epel 8.7 k readline ppc64le 8.1-4.el9 baseos 231 k rpm ppc64le 4.16.1.3-39.el9 baseos 534 k rpm-build-libs ppc64le 4.16.1.3-39.el9 baseos 96 k rpm-libs ppc64le 4.16.1.3-39.el9 baseos 351 k rpmautospec-rpm-macros noarch 0.8.1-11.el9 epel 11 k rust-srpm-macros noarch 17-4.el9 appstream 11 k rust-srpm-macros-epel noarch 26.3-1.el9 epel 10 k setup noarch 2.13.7-10.el9 baseos 150 k shadow-utils ppc64le 2:4.9-15.el9 baseos 1.2 M sqlite-libs ppc64le 3.34.1-9.el9_7 baseos 731 k systemd-libs ppc64le 252-55.el9_7.7 baseos 708 k tzdata noarch 2025c-1.el9 baseos 904 k util-linux-core ppc64le 2.37.4-21.el9 baseos 488 k xz-libs ppc64le 5.2.5-8.el9_0 baseos 117 k zip ppc64le 3.0-35.el9 baseos 276 k zlib ppc64le 1.2.11-40.el9 baseos 104 k zstd ppc64le 1.5.5-1.el9 baseos 407 k Transaction Summary ================================================================================ Install 211 Packages Total download size: 73 M Installed size: 276 M Downloading Packages: (1/211): cpio-2.13-16.el9.ppc64le.rpm 909 kB/s | 286 kB 00:00 (2/211): basesystem-11-13.el9.noarch.rpm 19 kB/s | 8.0 kB 00:00 (3/211): diffutils-3.7-12.el9.ppc64le.rpm 6.5 MB/s | 417 kB 00:00 (4/211): cracklib-dicts-2.9.6-27.el9.ppc64le.rp 20 MB/s | 3.6 MB 00:00 (5/211): cracklib-2.9.6-27.el9.ppc64le.rpm 199 kB/s | 100 kB 00:00 (6/211): ed-1.14.2-12.el9.ppc64le.rpm 2.8 MB/s | 81 kB 00:00 (7/211): groff-base-1.22.4-10.el9.ppc64le.rpm 14 MB/s | 1.1 MB 00:00 (8/211): gawk-5.1.0-6.el9.ppc64le.rpm 8.5 MB/s | 1.0 MB 00:00 (9/211): grep-3.6-5.el9.ppc64le.rpm 1.9 MB/s | 281 kB 00:00 (10/211): info-6.7-15.el9.ppc64le.rpm 3.7 MB/s | 256 kB 00:00 (11/211): json-c-0.14-11.el9.ppc64le.rpm 476 kB/s | 48 kB 00:00 (12/211): libcap-ng-0.8.2-7.el9.ppc64le.rpm 424 kB/s | 37 kB 00:00 (13/211): libgpg-error-1.42-5.el9.ppc64le.rpm 2.3 MB/s | 229 kB 00:00 (14/211): libidn2-2.3.0-7.el9.ppc64le.rpm 1.3 MB/s | 108 kB 00:00 (15/211): libattr-2.5.1-3.el9.ppc64le.rpm 116 kB/s | 21 kB 00:00 (16/211): libpwquality-1.4.4-8.el9.ppc64le.rpm 5.8 MB/s | 125 kB 00:00 (17/211): libsigsegv-2.13-4.el9.ppc64le.rpm 1.1 MB/s | 31 kB 00:00 (18/211): libunistring-0.9.10-15.el9.ppc64le.rp 17 MB/s | 507 kB 00:00 (19/211): libutempter-1.2.1-6.el9.ppc64le.rpm 1.4 MB/s | 30 kB 00:00 (20/211): libverto-0.3.2-3.el9.ppc64le.rpm 1.2 MB/s | 25 kB 00:00 (21/211): libxcrypt-4.4.18-3.el9.ppc64le.rpm 5.7 MB/s | 133 kB 00:00 (22/211): libpsl-0.21.1-5.el9.ppc64le.rpm 790 kB/s | 68 kB 00:00 (23/211): lz4-libs-1.9.3-5.el9.ppc64le.rpm 3.9 MB/s | 88 kB 00:00 (24/211): mpfr-4.1.0-7.el9.ppc64le.rpm 10 MB/s | 324 kB 00:00 (25/211): publicsuffix-list-dafsa-20210518-3.el 1.7 MB/s | 59 kB 00:00 (26/211): readline-8.1-4.el9.ppc64le.rpm 7.5 MB/s | 231 kB 00:00 (27/211): sed-4.8-9.el9.ppc64le.rpm 13 MB/s | 315 kB 00:00 (28/211): popt-1.18-8.el9.ppc64le.rpm 847 kB/s | 73 kB 00:00 (29/211): xz-5.2.5-8.el9_0.ppc64le.rpm 7.7 MB/s | 238 kB 00:00 (30/211): xz-libs-5.2.5-8.el9_0.ppc64le.rpm 2.6 MB/s | 117 kB 00:00 (31/211): keyutils-libs-1.6.3-1.el9.ppc64le.rpm 1.1 MB/s | 35 kB 00:00 (32/211): libpkgconf-1.7.3-10.el9.ppc64le.rpm 1.9 MB/s | 42 kB 00:00 (33/211): pkgconf-1.7.3-10.el9.ppc64le.rpm 1.5 MB/s | 45 kB 00:00 (34/211): pkgconf-m4-1.7.3-10.el9.noarch.rpm 768 kB/s | 16 kB 00:00 (35/211): zip-3.0-35.el9.ppc64le.rpm 9.2 MB/s | 276 kB 00:00 (36/211): pkgconf-pkg-config-1.7.3-10.el9.ppc64 316 kB/s | 12 kB 00:00 (37/211): gzip-1.12-1.el9.ppc64le.rpm 1.6 MB/s | 172 kB 00:00 (38/211): gmp-6.2.0-13.el9.ppc64le.rpm 11 MB/s | 305 kB 00:00 (39/211): zlib-1.2.11-40.el9.ppc64le.rpm 4.5 MB/s | 104 kB 00:00 (40/211): libffi-3.4.2-8.el9.ppc64le.rpm 683 kB/s | 40 kB 00:00 (41/211): lua-libs-5.4.4-4.el9.ppc64le.rpm 1.7 MB/s | 149 kB 00:00 (42/211): bash-5.1.8-9.el9.ppc64le.rpm 28 MB/s | 1.7 MB 00:00 (43/211): file-5.39-16.el9.ppc64le.rpm 1.0 MB/s | 52 kB 00:00 (44/211): setup-2.13.7-10.el9.noarch.rpm 6.1 MB/s | 150 kB 00:00 (45/211): libacl-2.3.1-4.el9.ppc64le.rpm 774 kB/s | 26 kB 00:00 (46/211): bzip2-1.0.8-10.el9_5.ppc64le.rpm 2.3 MB/s | 60 kB 00:00 (47/211): libevent-2.1.12-8.el9_4.ppc64le.rpm 7.3 MB/s | 281 kB 00:00 (48/211): file-libs-5.39-16.el9.ppc64le.rpm 6.1 MB/s | 604 kB 00:00 (49/211): bzip2-libs-1.0.8-10.el9_5.ppc64le.rpm 1.9 MB/s | 46 kB 00:00 (50/211): gdbm-libs-1.23-1.el9.ppc64le.rpm 1.0 MB/s | 64 kB 00:00 (51/211): filesystem-3.16-5.el9.ppc64le.rpm 40 MB/s | 4.8 MB 00:00 (52/211): libbrotli-1.0.9-7.el9_5.ppc64le.rpm 8.3 MB/s | 339 kB 00:00 (53/211): findutils-4.8.0-7.el9.ppc64le.rpm 5.0 MB/s | 589 kB 00:00 (54/211): libgcrypt-1.10.0-11.el9.ppc64le.rpm 18 MB/s | 599 kB 00:00 (55/211): libeconf-0.4.1-4.el9.ppc64le.rpm 777 kB/s | 32 kB 00:00 (56/211): p11-kit-0.25.3-3.el9_5.ppc64le.rpm 18 MB/s | 535 kB 00:00 (57/211): librtas-2.0.6-1.el9.ppc64le.rpm 2.5 MB/s | 84 kB 00:00 (58/211): pcre-8.44-4.el9.ppc64le.rpm 7.2 MB/s | 203 kB 00:00 (59/211): libnghttp2-1.43.0-6.el9.ppc64le.rpm 898 kB/s | 84 kB 00:00 (60/211): p11-kit-trust-0.25.3-3.el9_5.ppc64le. 3.0 MB/s | 157 kB 00:00 (61/211): pcre2-10.40-6.el9.ppc64le.rpm 7.1 MB/s | 237 kB 00:00 (62/211): alternatives-1.24-2.el9.ppc64le.rpm 1.6 MB/s | 43 kB 00:00 (63/211): libfdisk-2.37.4-21.el9.ppc64le.rpm 5.1 MB/s | 170 kB 00:00 (64/211): pcre2-syntax-10.40-6.el9.noarch.rpm 1.5 MB/s | 144 kB 00:00 (65/211): libmount-2.37.4-21.el9.ppc64le.rpm 1.6 MB/s | 153 kB 00:00 (66/211): libselinux-3.6-3.el9.ppc64le.rpm 1.1 MB/s | 100 kB 00:00 (67/211): libsemanage-3.6-5.el9_6.ppc64le.rpm 6.0 MB/s | 133 kB 00:00 (68/211): coreutils-common-8.32-39.el9.ppc64le. 11 MB/s | 2.0 MB 00:00 (69/211): libtool-ltdl-2.4.6-46.el9.ppc64le.rpm 1.8 MB/s | 41 kB 00:00 (70/211): openldap-2.6.8-4.el9.ppc64le.rpm 6.8 MB/s | 322 kB 00:00 (71/211): libzstd-1.5.5-1.el9.ppc64le.rpm 5.9 MB/s | 322 kB 00:00 (72/211): libsmartcols-2.37.4-21.el9.ppc64le.rp 798 kB/s | 70 kB 00:00 (73/211): util-linux-core-2.37.4-21.el9.ppc64le 14 MB/s | 488 kB 00:00 (74/211): util-linux-2.37.4-21.el9.ppc64le.rpm 36 MB/s | 2.3 MB 00:00 (75/211): coreutils-8.32-39.el9.ppc64le.rpm 27 MB/s | 1.2 MB 00:00 (76/211): zstd-1.5.5-1.el9.ppc64le.rpm 4.5 MB/s | 407 kB 00:00 (77/211): libblkid-2.37.4-21.el9.ppc64le.rpm 3.2 MB/s | 125 kB 00:00 (78/211): krb5-libs-1.21.1-8.el9_6.ppc64le.rpm 12 MB/s | 846 kB 00:00 (79/211): libuuid-2.37.4-21.el9.ppc64le.rpm 1.2 MB/s | 32 kB 00:00 (80/211): libtasn1-4.16.0-9.el9.ppc64le.rpm 2.2 MB/s | 82 kB 00:00 (81/211): libarchive-3.5.3-6.el9_6.ppc64le.rpm 13 MB/s | 454 kB 00:00 (82/211): pam-1.5.1-26.el9_6.ppc64le.rpm 16 MB/s | 662 kB 00:00 (83/211): libdb-5.3.28-57.el9_6.ppc64le.rpm 7.1 MB/s | 817 kB 00:00 (84/211): which-2.21-30.el9_6.ppc64le.rpm 1.5 MB/s | 42 kB 00:00 (85/211): audit-libs-3.1.5-7.el9.ppc64le.rpm 5.5 MB/s | 137 kB 00:00 (86/211): curl-7.76.1-34.el9.ppc64le.rpm 6.3 MB/s | 295 kB 00:00 (87/211): crypto-policies-20250905-1.git377cc42 1.0 MB/s | 90 kB 00:00 (88/211): elfutils-0.193-1.el9.ppc64le.rpm 9.9 MB/s | 601 kB 00:00 (89/211): cyrus-sasl-lib-2.1.27-22.el9.ppc64le. 7.3 MB/s | 856 kB 00:00 (90/211): elfutils-default-yama-scope-0.193-1.e 198 kB/s | 9.7 kB 00:00 (91/211): elfutils-debuginfod-client-0.193-1.el 538 kB/s | 46 kB 00:00 (92/211): elfutils-libelf-0.193-1.el9.ppc64le.r 4.1 MB/s | 211 kB 00:00 (93/211): elfutils-libs-0.193-1.el9.ppc64le.rpm 7.0 MB/s | 305 kB 00:00 (94/211): libcurl-7.76.1-34.el9.ppc64le.rpm 11 MB/s | 314 kB 00:00 (95/211): libcap-2.48-10.el9.ppc64le.rpm 864 kB/s | 74 kB 00:00 (96/211): libgcc-11.5.0-11.el9.ppc64le.rpm 2.5 MB/s | 74 kB 00:00 (97/211): libcom_err-1.46.5-8.el9.ppc64le.rpm 251 kB/s | 27 kB 00:00 (98/211): libsepol-3.6-3.el9.ppc64le.rpm 10 MB/s | 366 kB 00:00 (99/211): libstdc++-11.5.0-11.el9.ppc64le.rpm 12 MB/s | 837 kB 00:00 (100/211): ncurses-6.2-12.20210508.el9.ppc64le. 7.3 MB/s | 413 kB 00:00 (101/211): libgomp-11.5.0-11.el9.ppc64le.rpm 2.3 MB/s | 269 kB 00:00 (102/211): ncurses-base-6.2-12.20210508.el9.noa 4.4 MB/s | 96 kB 00:00 (103/211): ncurses-libs-6.2-12.20210508.el9.ppc 14 MB/s | 370 kB 00:00 (104/211): rpm-4.16.1.3-39.el9.ppc64le.rpm 15 MB/s | 534 kB 00:00 (105/211): openssl-fips-provider-so-3.0.7-8.el9 12 MB/s | 563 kB 00:00 (106/211): openssl-fips-provider-3.0.7-8.el9.pp 108 kB/s | 9.2 kB 00:00 (107/211): rpm-build-libs-4.16.1.3-39.el9.ppc64 2.9 MB/s | 96 kB 00:00 (108/211): rpm-libs-4.16.1.3-39.el9.ppc64le.rpm 10 MB/s | 351 kB 00:00 (109/211): unzip-6.0-59.el9.ppc64le.rpm 3.7 MB/s | 186 kB 00:00 (110/211): glibc-2.34-231.el9_7.2.ppc64le.rpm 39 MB/s | 2.7 MB 00:00 (111/211): glibc-common-2.34-231.el9_7.2.ppc64l 9.5 MB/s | 323 kB 00:00 (112/211): shadow-utils-4.9-15.el9.ppc64le.rpm 12 MB/s | 1.2 MB 00:00 (113/211): glibc-minimal-langpack-2.34-231.el9_ 1.0 MB/s | 22 kB 00:00 (114/211): glibc-gconv-extra-2.34-231.el9_7.2.p 33 MB/s | 1.7 MB 00:00 (115/211): sqlite-libs-3.34.1-9.el9_7.ppc64le.r 15 MB/s | 731 kB 00:00 (116/211): ca-certificates-2025.2.80_v9.0.305-9 26 MB/s | 1.0 MB 00:00 (117/211): redhat-release-9.7-0.7.el9.ppc64le.r 617 kB/s | 53 kB 00:00 (118/211): systemd-libs-252-55.el9_7.7.ppc64le. 20 MB/s | 708 kB 00:00 (119/211): libssh-0.10.4-17.el9_7.ppc64le.rpm 9.7 MB/s | 238 kB 00:00 (120/211): libssh-config-0.10.4-17.el9_7.noarch 393 kB/s | 8.1 kB 00:00 (121/211): libxml2-2.9.13-14.el9_7.ppc64le.rpm 5.2 MB/s | 823 kB 00:00 (122/211): binutils-2.35.2-67.el9_7.1.ppc64le.r 48 MB/s | 5.0 MB 00:00 (123/211): tzdata-2025c-1.el9.noarch.rpm 4.8 MB/s | 904 kB 00:00 (124/211): binutils-gold-2.35.2-67.el9_7.1.ppc6 15 MB/s | 1.0 MB 00:00 (125/211): tar-1.34-9.el9_7.ppc64le.rpm 25 MB/s | 916 kB 00:00 (126/211): openssl-libs-3.5.1-5.el9_7.ppc64le.r 42 MB/s | 2.4 MB 00:00 (127/211): perl-Encode-3.08-462.el9.ppc64le.rpm 25 MB/s | 1.7 MB 00:00 (128/211): perl-Exporter-5.74-461.el9.noarch.rp 1.0 MB/s | 34 kB 00:00 (129/211): openssl-3.5.1-5.el9_7.ppc64le.rpm 13 MB/s | 1.5 MB 00:00 (130/211): perl-MIME-Base64-3.16-4.el9.ppc64le. 1.4 MB/s | 35 kB 00:00 (131/211): perl-File-Temp-0.231.100-4.el9.noarc 1.5 MB/s | 63 kB 00:00 (132/211): perl-Term-Cap-1.17-460.el9.noarch.rp 1.1 MB/s | 24 kB 00:00 (133/211): perl-Socket-2.031-4.el9.ppc64le.rpm 1.1 MB/s | 59 kB 00:00 (134/211): perl-Time-Local-1.300-7.el9.noarch.r 1.3 MB/s | 37 kB 00:00 (135/211): perl-Mozilla-CA-20200520-6.el9.noarc 157 kB/s | 14 kB 00:00 (136/211): perl-srpm-macros-1-41.el9.noarch.rpm 252 kB/s | 9.4 kB 00:00 (137/211): perl-parent-0.238-460.el9.noarch.rpm 326 kB/s | 16 kB 00:00 (138/211): lua-srpm-macros-1-6.el9.noarch.rpm 412 kB/s | 10 kB 00:00 (139/211): ghc-srpm-macros-1.5.0-6.el9.noarch.r 327 kB/s | 9.0 kB 00:00 (140/211): perl-Digest-MD5-2.58-4.el9.ppc64le.r 1.7 MB/s | 40 kB 00:00 (141/211): patch-2.7.6-16.el9.ppc64le.rpm 5.1 MB/s | 140 kB 00:00 (142/211): rust-srpm-macros-17-4.el9.noarch.rpm 133 kB/s | 11 kB 00:00 (143/211): perl-IO-Socket-IP-0.41-5.el9.noarch. 2.1 MB/s | 45 kB 00:00 (144/211): perl-Pod-Escapes-1.07-460.el9.noarch 883 kB/s | 22 kB 00:00 (145/211): perl-Term-ANSIColor-5.01-461.el9.noa 2.3 MB/s | 51 kB 00:00 (146/211): perl-Text-ParseWords-3.30-460.el9.no 445 kB/s | 18 kB 00:00 (147/211): perl-Text-Tabs+Wrap-2013.0523-460.el 516 kB/s | 25 kB 00:00 (148/211): perl-URI-5.09-3.el9.noarch.rpm 4.8 MB/s | 125 kB 00:00 (149/211): perl-Pod-Simple-3.42-4.el9.noarch.rp 2.5 MB/s | 229 kB 00:00 (150/211): openblas-srpm-macros-2-11.el9.noarch 344 kB/s | 8.6 kB 00:00 (151/211): perl-constant-1.33-461.el9.noarch.rp 640 kB/s | 25 kB 00:00 (152/211): perl-File-Path-2.18-4.el9.noarch.rpm 1.2 MB/s | 38 kB 00:00 (153/211): perl-Pod-Perldoc-3.28.01-461.el9.noa 3.8 MB/s | 92 kB 00:00 (154/211): perl-Pod-Usage-2.01-4.el9.noarch.rpm 1.2 MB/s | 43 kB 00:00 (155/211): perl-libnet-3.13-4.el9.noarch.rpm 4.2 MB/s | 134 kB 00:00 (156/211): perl-Data-Dumper-2.174-462.el9.ppc64 553 kB/s | 59 kB 00:00 (157/211): fonts-srpm-macros-2.0.5-7.el9.1.noar 1.3 MB/s | 29 kB 00:00 (158/211): perl-Carp-1.50-460.el9.noarch.rpm 768 kB/s | 31 kB 00:00 (159/211): perl-Digest-1.19-4.el9.noarch.rpm 977 kB/s | 29 kB 00:00 (160/211): perl-podlators-4.14-460.el9.noarch.r 1.2 MB/s | 118 kB 00:00 (161/211): perl-Getopt-Long-2.52-4.el9.noarch.r 2.3 MB/s | 64 kB 00:00 (162/211): ocaml-srpm-macros-6-6.el9.noarch.rpm 87 kB/s | 9.1 kB 00:00 (163/211): perl-PathTools-3.78-461.el9.ppc64le. 3.0 MB/s | 93 kB 00:00 (164/211): perl-HTTP-Tiny-0.076-462.el9.noarch. 2.6 MB/s | 57 kB 00:00 (165/211): perl-Storable-3.21-460.el9.ppc64le.r 1.0 MB/s | 101 kB 00:00 (166/211): perl-Scalar-List-Utils-1.56-462.el9. 2.8 MB/s | 78 kB 00:00 (167/211): qt5-srpm-macros-5.15.9-1.el9.noarch. 109 kB/s | 9.1 kB 00:00 (168/211): perl-IO-Socket-SSL-2.073-2.el9.noarc 8.1 MB/s | 221 kB 00:00 (169/211): python-srpm-macros-3.9-54.el9.noarch 702 kB/s | 18 kB 00:00 (170/211): perl-AutoLoader-5.74-481.1.el9_6.noa 513 kB/s | 21 kB 00:00 (171/211): perl-B-1.80-481.1.el9_6.ppc64le.rpm 5.2 MB/s | 183 kB 00:00 (172/211): perl-Errno-1.30-481.1.el9_6.ppc64le. 631 kB/s | 14 kB 00:00 (173/211): pyproject-srpm-macros-1.16.2-1.el9.n 164 kB/s | 14 kB 00:00 (174/211): perl-Class-Struct-0.66-481.1.el9_6.n 448 kB/s | 22 kB 00:00 (175/211): perl-Fcntl-1.13-481.1.el9_6.ppc64le. 824 kB/s | 20 kB 00:00 (176/211): perl-FileHandle-2.03-481.1.el9_6.noa 552 kB/s | 15 kB 00:00 (177/211): perl-Getopt-Std-1.12-481.1.el9_6.noa 704 kB/s | 15 kB 00:00 (178/211): perl-File-stat-1.09-481.1.el9_6.noar 240 kB/s | 17 kB 00:00 (179/211): perl-File-Basename-2.85-481.1.el9_6. 200 kB/s | 17 kB 00:00 (180/211): perl-IO-1.43-481.1.el9_6.ppc64le.rpm 3.9 MB/s | 89 kB 00:00 (181/211): perl-SelectSaver-1.02-481.1.el9_6.no 400 kB/s | 11 kB 00:00 (182/211): perl-IPC-Open3-1.21-481.1.el9_6.noar 590 kB/s | 22 kB 00:00 (183/211): perl-Symbol-1.08-481.1.el9_6.noarch. 546 kB/s | 14 kB 00:00 (184/211): perl-base-2.27-481.1.el9_6.noarch.rp 481 kB/s | 16 kB 00:00 (185/211): perl-if-0.60.800-481.1.el9_6.noarch. 438 kB/s | 14 kB 00:00 (186/211): perl-POSIX-1.94-481.1.el9_6.ppc64le. 1.0 MB/s | 98 kB 00:00 (187/211): perl-libs-5.32.1-481.1.el9_6.ppc64le 36 MB/s | 2.3 MB 00:00 (188/211): perl-mro-1.23-481.1.el9_6.ppc64le.rp 340 kB/s | 28 kB 00:00 (189/211): perl-overload-1.31-481.1.el9_6.noarc 1.7 MB/s | 45 kB 00:00 (190/211): perl-subs-1.03-481.1.el9_6.noarch.rp 367 kB/s | 11 kB 00:00 (191/211): perl-interpreter-5.32.1-481.1.el9_6. 497 kB/s | 70 kB 00:00 (192/211): perl-vars-1.05-481.1.el9_6.noarch.rp 523 kB/s | 13 kB 00:00 (193/211): efi-srpm-macros-6-4.el9.noarch.rpm 419 kB/s | 21 kB 00:00 (194/211): perl-overloading-0.02-481.1.el9_6.no 129 kB/s | 12 kB 00:00 (195/211): redhat-rpm-config-210-1.el9.noarch.r 1.9 MB/s | 70 kB 00:00 (196/211): gdb-minimal-16.3-2.el9.ppc64le.rpm 41 MB/s | 4.6 MB 00:00 (197/211): debugedit-5.0-11.el9.ppc64le.rpm 1.4 MB/s | 81 kB 00:00 (198/211): rpm-build-4.16.1.3-39.el9.ppc64le.rp 783 kB/s | 67 kB 00:00 (199/211): dwz-0.16-1.el9.ppc64le.rpm 4.6 MB/s | 140 kB 00:00 (200/211): kernel-srpm-macros-1.0-14.el9.noarch 376 kB/s | 14 kB 00:00 (201/211): go-srpm-macros-3.6.0-12.el9_7.noarch 1.1 MB/s | 27 kB 00:00 (202/211): perl-Net-SSLeay-1.94-3.el9.ppc64le.r 4.4 MB/s | 423 kB 00:00 [MIRROR] ansible-srpm-macros-1-16.el9.noarch.rpm: Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/epel/9/Everything/ppc64le/Packages/a/ansible-srpm-macros-1-16.el9.noarch.rpm [Failed to connect to dl.fedoraproject.org port 443: Connection timed out] [MIRROR] epel-rpm-macros-9-17.el9.noarch.rpm: Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/epel/9/Everything/ppc64le/Packages/e/epel-rpm-macros-9-17.el9.noarch.rpm [Failed to connect to dl.fedoraproject.org port 443: Connection timed out] [MIRROR] forge-srpm-macros-0.4.0-1.el9.noarch.rpm: Curl error (28): Timeout was reached for https://dl.fedoraproject.org/pub/epel/9/Everything/ppc64le/Packages/f/forge-srpm-macros-0.4.0-1.el9.noarch.rpm [Failed to connect to dl.fedoraproject.org port 443: Connection timed out] (203/211): ansible-srpm-macros-1-16.el9.noarch. 720 B/s | 21 kB 00:29 (204/211): epel-rpm-macros-9-17.el9.noarch.rpm 522 B/s | 15 kB 00:29 (205/211): forge-srpm-macros-0.4.0-1.el9.noarch 677 B/s | 19 kB 00:29 (206/211): fpc-srpm-macros-1.3-7.el9.noarch.rpm 101 kB/s | 7.5 kB 00:00 (207/211): ghc-srpm-macros-epel-1.9.1-1.el9.noa 101 kB/s | 7.5 kB 00:00 (208/211): go-srpm-macros-epel-3.8.0-1.el9.noar 360 kB/s | 26 kB 00:00 (209/211): rpmautospec-rpm-macros-0.8.1-11.el9. 152 kB/s | 11 kB 00:00 (210/211): qt6-srpm-macros-6.6.2-1.el9.noarch.r 117 kB/s | 8.7 kB 00:00 (211/211): rust-srpm-macros-epel-26.3-1.el9.noa 141 kB/s | 10 kB 00:00 -------------------------------------------------------------------------------- Total 2.2 MB/s | 73 MB 00:33 Red Hat Enterprise Linux - BaseOS 3.5 MB/s | 3.6 kB 00:00 Importing GPG key 0xFD431D51: Userid : "Red Hat, Inc. (release key 2) " Fingerprint: 567E 347A D004 4ADE 55BA 8A5F 199E 2F91 FD43 1D51 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat9-release Key imported successfully Importing GPG key 0x5A6340B3: Userid : "Red Hat, Inc. (auxiliary key 3) " Fingerprint: 7E46 2425 8C40 6535 D56D 6F13 5054 E4A4 5A63 40B3 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat9-release Key imported successfully Extra Packages for Enterprise Linux 9 - ppc64le 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x3228467C: Userid : "Fedora (epel9) " Fingerprint: FF8A D134 4597 106E CE81 3B91 8A38 72BF 3228 467C From : /usr/share/distribution-gpg-keys/epel/RPM-GPG-KEY-EPEL-9 Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.16-5.el9.ppc64le 1/1 Preparing : 1/1 Installing : rust-srpm-macros-17-4.el9.noarch 1/211 Installing : redhat-release-9.7-0.7.el9.ppc64le 2/211 Installing : setup-2.13.7-10.el9.noarch 3/211 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.13.7-10.el9.noarch 3/211 Installing : filesystem-3.16-5.el9.ppc64le 4/211 Installing : basesystem-11-13.el9.noarch 5/211 Installing : rust-srpm-macros-epel-26.3-1.el9.noarch 6/211 Installing : qt6-srpm-macros-6.6.2-1.el9.noarch 7/211 Installing : ghc-srpm-macros-epel-1.9.1-1.el9.noarch 8/211 Installing : fpc-srpm-macros-1.3-7.el9.noarch 9/211 Installing : ansible-srpm-macros-1-16.el9.noarch 10/211 Installing : qt5-srpm-macros-5.15.9-1.el9.noarch 11/211 Installing : ocaml-srpm-macros-6-6.el9.noarch 12/211 Installing : openblas-srpm-macros-2-11.el9.noarch 13/211 Installing : ghc-srpm-macros-1.5.0-6.el9.noarch 14/211 Installing : perl-srpm-macros-1-41.el9.noarch 15/211 Installing : libssh-config-0.10.4-17.el9_7.noarch 16/211 Installing : tzdata-2025c-1.el9.noarch 17/211 Installing : ncurses-base-6.2-12.20210508.el9.noarch 18/211 Installing : ncurses-libs-6.2-12.20210508.el9.ppc64le 19/211 Installing : bash-5.1.8-9.el9.ppc64le 20/211 Running scriptlet: bash-5.1.8-9.el9.ppc64le 20/211 Installing : libgcc-11.5.0-11.el9.ppc64le 21/211 Running scriptlet: libgcc-11.5.0-11.el9.ppc64le 21/211 Installing : glibc-common-2.34-231.el9_7.2.ppc64le 22/211 Installing : glibc-gconv-extra-2.34-231.el9_7.2.ppc64le 23/211 Running scriptlet: glibc-gconv-extra-2.34-231.el9_7.2.ppc64le 23/211 Installing : glibc-minimal-langpack-2.34-231.el9_7.2.ppc64le 24/211 Running scriptlet: glibc-2.34-231.el9_7.2.ppc64le 25/211 Installing : glibc-2.34-231.el9_7.2.ppc64le 25/211 Running scriptlet: glibc-2.34-231.el9_7.2.ppc64le 25/211 Installing : zlib-1.2.11-40.el9.ppc64le 26/211 Installing : xz-libs-5.2.5-8.el9_0.ppc64le 27/211 Installing : bzip2-libs-1.0.8-10.el9_5.ppc64le 28/211 Installing : libzstd-1.5.5-1.el9.ppc64le 29/211 Installing : elfutils-libelf-0.193-1.el9.ppc64le 30/211 Installing : libxcrypt-4.4.18-3.el9.ppc64le 31/211 Installing : libuuid-2.37.4-21.el9.ppc64le 32/211 Installing : libstdc++-11.5.0-11.el9.ppc64le 33/211 Installing : libattr-2.5.1-3.el9.ppc64le 34/211 Installing : libacl-2.3.1-4.el9.ppc64le 35/211 Installing : popt-1.18-8.el9.ppc64le 36/211 Installing : gmp-1:6.2.0-13.el9.ppc64le 37/211 Installing : libcap-2.48-10.el9.ppc64le 38/211 Installing : lz4-libs-1.9.3-5.el9.ppc64le 39/211 Installing : readline-8.1-4.el9.ppc64le 40/211 Installing : libcom_err-1.46.5-8.el9.ppc64le 41/211 Installing : crypto-policies-20250905-1.git377cc42.el9_7.noar 42/211 Running scriptlet: crypto-policies-20250905-1.git377cc42.el9_7.noar 42/211 Installing : mpfr-4.1.0-7.el9.ppc64le 43/211 Installing : dwz-0.16-1.el9.ppc64le 44/211 Installing : unzip-6.0-59.el9.ppc64le 45/211 Installing : file-libs-5.39-16.el9.ppc64le 46/211 Installing : file-5.39-16.el9.ppc64le 47/211 Installing : sqlite-libs-3.34.1-9.el9_7.ppc64le 48/211 Installing : libcap-ng-0.8.2-7.el9.ppc64le 49/211 Installing : audit-libs-3.1.5-7.el9.ppc64le 50/211 Installing : libsigsegv-2.13-4.el9.ppc64le 51/211 Installing : gawk-5.1.0-6.el9.ppc64le 52/211 Installing : libunistring-0.9.10-15.el9.ppc64le 53/211 Installing : libidn2-2.3.0-7.el9.ppc64le 54/211 Installing : libffi-3.4.2-8.el9.ppc64le 55/211 Installing : lua-libs-5.4.4-4.el9.ppc64le 56/211 Installing : alternatives-1.24-2.el9.ppc64le 57/211 Installing : libsmartcols-2.37.4-21.el9.ppc64le 58/211 Installing : libtasn1-4.16.0-9.el9.ppc64le 59/211 Installing : p11-kit-0.25.3-3.el9_5.ppc64le 60/211 Installing : libsepol-3.6-3.el9.ppc64le 61/211 Installing : p11-kit-trust-0.25.3-3.el9_5.ppc64le 62/211 Running scriptlet: p11-kit-trust-0.25.3-3.el9_5.ppc64le 62/211 Installing : zip-3.0-35.el9.ppc64le 63/211 Installing : zstd-1.5.5-1.el9.ppc64le 64/211 Running scriptlet: groff-base-1.22.4-10.el9.ppc64le 65/211 Installing : groff-base-1.22.4-10.el9.ppc64le 65/211 Running scriptlet: groff-base-1.22.4-10.el9.ppc64le 65/211 Installing : bzip2-1.0.8-10.el9_5.ppc64le 66/211 Installing : libxml2-2.9.13-14.el9_7.ppc64le 67/211 Installing : info-6.7-15.el9.ppc64le 68/211 Installing : ed-1.14.2-12.el9.ppc64le 69/211 Installing : cpio-2.13-16.el9.ppc64le 70/211 Installing : diffutils-3.7-12.el9.ppc64le 71/211 Installing : json-c-0.14-11.el9.ppc64le 72/211 Installing : libgpg-error-1.42-5.el9.ppc64le 73/211 Installing : libgcrypt-1.10.0-11.el9.ppc64le 74/211 Installing : libverto-0.3.2-3.el9.ppc64le 75/211 Installing : keyutils-libs-1.6.3-1.el9.ppc64le 76/211 Installing : libpkgconf-1.7.3-10.el9.ppc64le 77/211 Installing : pkgconf-1.7.3-10.el9.ppc64le 78/211 Installing : gdbm-libs-1:1.23-1.el9.ppc64le 79/211 Installing : libbrotli-1.0.9-7.el9_5.ppc64le 80/211 Installing : libeconf-0.4.1-4.el9.ppc64le 81/211 Installing : libnghttp2-1.43.0-6.el9.ppc64le 82/211 Installing : librtas-2.0.6-1.el9.ppc64le 83/211 Running scriptlet: librtas-2.0.6-1.el9.ppc64le 83/211 Installing : pcre-8.44-4.el9.ppc64le 84/211 Installing : grep-3.6-5.el9.ppc64le 85/211 Installing : xz-5.2.5-8.el9_0.ppc64le 86/211 Installing : libtool-ltdl-2.4.6-46.el9.ppc64le 87/211 Installing : libdb-5.3.28-57.el9_6.ppc64le 88/211 Installing : libgomp-11.5.0-11.el9.ppc64le 89/211 Installing : ncurses-6.2-12.20210508.el9.ppc64le 90/211 Installing : elfutils-default-yama-scope-0.193-1.el9.noarch 91/211 Running scriptlet: elfutils-default-yama-scope-0.193-1.el9.noarch 91/211 Installing : elfutils-libs-0.193-1.el9.ppc64le 92/211 Installing : coreutils-common-8.32-39.el9.ppc64le 93/211 Installing : pcre2-syntax-10.40-6.el9.noarch 94/211 Installing : pcre2-10.40-6.el9.ppc64le 95/211 Installing : libselinux-3.6-3.el9.ppc64le 96/211 Installing : sed-4.8-9.el9.ppc64le 97/211 Installing : findutils-1:4.8.0-7.el9.ppc64le 98/211 Installing : openssl-fips-provider-so-3.0.7-8.el9.ppc64le 99/211 Installing : openssl-fips-provider-3.0.7-8.el9.ppc64le 100/211 Installing : openssl-libs-1:3.5.1-5.el9_7.ppc64le 101/211 Installing : coreutils-8.32-39.el9.ppc64le 102/211 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-91.el9.noarch 103/211 Installing : ca-certificates-2025.2.80_v9.0.305-91.el9.noarch 103/211 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-91.el9.noarch 103/211 Installing : libblkid-2.37.4-21.el9.ppc64le 104/211 Running scriptlet: libblkid-2.37.4-21.el9.ppc64le 104/211 Installing : krb5-libs-1.21.1-8.el9_6.ppc64le 105/211 Installing : libmount-2.37.4-21.el9.ppc64le 106/211 Installing : gzip-1.12-1.el9.ppc64le 107/211 Installing : cracklib-2.9.6-27.el9.ppc64le 108/211 Installing : systemd-libs-252-55.el9_7.7.ppc64le 109/211 Running scriptlet: systemd-libs-252-55.el9_7.7.ppc64le 109/211 Installing : libarchive-3.5.3-6.el9_6.ppc64le 110/211 Installing : util-linux-core-2.37.4-21.el9.ppc64le 111/211 Running scriptlet: util-linux-core-2.37.4-21.el9.ppc64le 111/211 Installing : cracklib-dicts-2.9.6-27.el9.ppc64le 112/211 Installing : cyrus-sasl-lib-2.1.27-22.el9.ppc64le 113/211 Installing : libssh-0.10.4-17.el9_7.ppc64le 114/211 Installing : libfdisk-2.37.4-21.el9.ppc64le 115/211 Installing : perl-Digest-1.19-4.el9.noarch 116/211 Installing : perl-Digest-MD5-2.58-4.el9.ppc64le 117/211 Installing : perl-B-1.80-481.1.el9_6.ppc64le 118/211 Installing : perl-FileHandle-2.03-481.1.el9_6.noarch 119/211 Installing : perl-Data-Dumper-2.174-462.el9.ppc64le 120/211 Installing : perl-libnet-3.13-4.el9.noarch 121/211 Installing : perl-AutoLoader-5.74-481.1.el9_6.noarch 122/211 Installing : perl-base-2.27-481.1.el9_6.noarch 123/211 Installing : perl-URI-5.09-3.el9.noarch 124/211 Installing : perl-Time-Local-2:1.300-7.el9.noarch 125/211 Installing : perl-Mozilla-CA-20200520-6.el9.noarch 126/211 Installing : perl-if-0.60.800-481.1.el9_6.noarch 127/211 Installing : perl-IO-Socket-IP-0.41-5.el9.noarch 128/211 Installing : perl-Pod-Escapes-1:1.07-460.el9.noarch 129/211 Installing : perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch 130/211 Installing : perl-File-Path-2.18-4.el9.noarch 131/211 Installing : perl-IO-Socket-SSL-2.073-2.el9.noarch 132/211 Installing : perl-Net-SSLeay-1.94-3.el9.ppc64le 133/211 Installing : perl-Term-ANSIColor-5.01-461.el9.noarch 134/211 Installing : perl-Class-Struct-0.66-481.1.el9_6.noarch 135/211 Installing : perl-POSIX-1.94-481.1.el9_6.ppc64le 136/211 Installing : perl-IPC-Open3-1.21-481.1.el9_6.noarch 137/211 Installing : perl-subs-1.03-481.1.el9_6.noarch 138/211 Installing : perl-Term-Cap-1.17-460.el9.noarch 139/211 Installing : perl-File-Temp-1:0.231.100-4.el9.noarch 140/211 Installing : perl-Pod-Simple-1:3.42-4.el9.noarch 141/211 Installing : perl-HTTP-Tiny-0.076-462.el9.noarch 142/211 Installing : perl-Socket-4:2.031-4.el9.ppc64le 143/211 Installing : perl-SelectSaver-1.02-481.1.el9_6.noarch 144/211 Installing : perl-Symbol-1.08-481.1.el9_6.noarch 145/211 Installing : perl-File-stat-1.09-481.1.el9_6.noarch 146/211 Installing : perl-podlators-1:4.14-460.el9.noarch 147/211 Installing : perl-Pod-Perldoc-3.28.01-461.el9.noarch 148/211 Installing : perl-Text-ParseWords-3.30-460.el9.noarch 149/211 Installing : perl-Fcntl-1.13-481.1.el9_6.ppc64le 150/211 Installing : perl-mro-1.23-481.1.el9_6.ppc64le 151/211 Installing : perl-IO-1.43-481.1.el9_6.ppc64le 152/211 Installing : perl-overloading-0.02-481.1.el9_6.noarch 153/211 Installing : perl-Pod-Usage-4:2.01-4.el9.noarch 154/211 Installing : perl-parent-1:0.238-460.el9.noarch 155/211 Installing : perl-MIME-Base64-3.16-4.el9.ppc64le 156/211 Installing : perl-constant-1.33-461.el9.noarch 157/211 Installing : perl-Scalar-List-Utils-4:1.56-462.el9.ppc64le 158/211 Installing : perl-Errno-1.30-481.1.el9_6.ppc64le 159/211 Installing : perl-File-Basename-2.85-481.1.el9_6.noarch 160/211 Installing : perl-Getopt-Std-1.12-481.1.el9_6.noarch 161/211 Installing : perl-Storable-1:3.21-460.el9.ppc64le 162/211 Installing : perl-overload-1.31-481.1.el9_6.noarch 163/211 Installing : perl-vars-1.05-481.1.el9_6.noarch 164/211 Installing : perl-Getopt-Long-1:2.52-4.el9.noarch 165/211 Installing : perl-Exporter-5.74-461.el9.noarch 166/211 Installing : perl-Carp-1.50-460.el9.noarch 167/211 Installing : perl-PathTools-3.78-461.el9.ppc64le 168/211 Installing : perl-Encode-4:3.08-462.el9.ppc64le 169/211 Installing : perl-libs-4:5.32.1-481.1.el9_6.ppc64le 170/211 Installing : perl-interpreter-4:5.32.1-481.1.el9_6.ppc64le 171/211 Installing : kernel-srpm-macros-1.0-14.el9.noarch 172/211 Installing : openssl-1:3.5.1-5.el9_7.ppc64le 173/211 Installing : libpwquality-1.4.4-8.el9.ppc64le 174/211 Installing : pam-1.5.1-26.el9_6.ppc64le 175/211 Installing : libevent-2.1.12-8.el9_4.ppc64le 176/211 Installing : libsemanage-3.6-5.el9_6.ppc64le 177/211 Installing : shadow-utils-2:4.9-15.el9.ppc64le 178/211 Running scriptlet: libutempter-1.2.1-6.el9.ppc64le 179/211 Installing : libutempter-1.2.1-6.el9.ppc64le 179/211 Installing : openldap-2.6.8-4.el9.ppc64le 180/211 Installing : tar-2:1.34-9.el9_7.ppc64le 181/211 Installing : patch-2.7.6-16.el9.ppc64le 182/211 Installing : pkgconf-m4-1.7.3-10.el9.noarch 183/211 Installing : pkgconf-pkg-config-1.7.3-10.el9.ppc64le 184/211 Installing : publicsuffix-list-dafsa-20210518-3.el9.noarch 185/211 Installing : libpsl-0.21.1-5.el9.ppc64le 186/211 Installing : libcurl-7.76.1-34.el9.ppc64le 187/211 Installing : elfutils-debuginfod-client-0.193-1.el9.ppc64le 188/211 Installing : binutils-gold-2.35.2-67.el9_7.1.ppc64le 189/211 Installing : binutils-2.35.2-67.el9_7.1.ppc64le 190/211 Running scriptlet: binutils-2.35.2-67.el9_7.1.ppc64le 190/211 Installing : elfutils-0.193-1.el9.ppc64le 191/211 Installing : gdb-minimal-16.3-2.el9.ppc64le 192/211 Installing : debugedit-5.0-11.el9.ppc64le 193/211 Installing : curl-7.76.1-34.el9.ppc64le 194/211 Installing : rpm-libs-4.16.1.3-39.el9.ppc64le 195/211 Installing : rpm-4.16.1.3-39.el9.ppc64le 196/211 Installing : lua-srpm-macros-1-6.el9.noarch 197/211 Installing : efi-srpm-macros-6-4.el9.noarch 198/211 Installing : rpmautospec-rpm-macros-0.8.1-11.el9.noarch 199/211 Installing : rpm-build-libs-4.16.1.3-39.el9.ppc64le 200/211 Installing : fonts-srpm-macros-1:2.0.5-7.el9.1.noarch 201/211 Installing : python-srpm-macros-3.9-54.el9.noarch 202/211 Installing : pyproject-srpm-macros-1.16.2-1.el9.noarch 203/211 Installing : rpm-build-4.16.1.3-39.el9.ppc64le 204/211 Installing : go-srpm-macros-3.6.0-12.el9_7.noarch 205/211 Installing : redhat-rpm-config-210-1.el9.noarch 206/211 Installing : forge-srpm-macros-0.4.0-1.el9.noarch 207/211 Installing : go-srpm-macros-epel-3.8.0-1.el9.noarch 208/211 Installing : epel-rpm-macros-9-17.el9.noarch 209/211 Installing : util-linux-2.37.4-21.el9.ppc64le 210/211 Installing : which-2.21-30.el9_6.ppc64le 211/211 Running scriptlet: filesystem-3.16-5.el9.ppc64le 211/211 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-91.el9.noarch 211/211 Running scriptlet: rpm-4.16.1.3-39.el9.ppc64le 211/211 Running scriptlet: which-2.21-30.el9_6.ppc64le 211/211 Verifying : basesystem-11-13.el9.noarch 1/211 Verifying : cpio-2.13-16.el9.ppc64le 2/211 Verifying : cracklib-2.9.6-27.el9.ppc64le 3/211 Verifying : cracklib-dicts-2.9.6-27.el9.ppc64le 4/211 Verifying : diffutils-3.7-12.el9.ppc64le 5/211 Verifying : ed-1.14.2-12.el9.ppc64le 6/211 Verifying : gawk-5.1.0-6.el9.ppc64le 7/211 Verifying : grep-3.6-5.el9.ppc64le 8/211 Verifying : groff-base-1.22.4-10.el9.ppc64le 9/211 Verifying : info-6.7-15.el9.ppc64le 10/211 Verifying : json-c-0.14-11.el9.ppc64le 11/211 Verifying : libattr-2.5.1-3.el9.ppc64le 12/211 Verifying : libcap-ng-0.8.2-7.el9.ppc64le 13/211 Verifying : libgpg-error-1.42-5.el9.ppc64le 14/211 Verifying : libidn2-2.3.0-7.el9.ppc64le 15/211 Verifying : libpsl-0.21.1-5.el9.ppc64le 16/211 Verifying : libpwquality-1.4.4-8.el9.ppc64le 17/211 Verifying : libsigsegv-2.13-4.el9.ppc64le 18/211 Verifying : libunistring-0.9.10-15.el9.ppc64le 19/211 Verifying : libutempter-1.2.1-6.el9.ppc64le 20/211 Verifying : libverto-0.3.2-3.el9.ppc64le 21/211 Verifying : libxcrypt-4.4.18-3.el9.ppc64le 22/211 Verifying : lz4-libs-1.9.3-5.el9.ppc64le 23/211 Verifying : mpfr-4.1.0-7.el9.ppc64le 24/211 Verifying : popt-1.18-8.el9.ppc64le 25/211 Verifying : publicsuffix-list-dafsa-20210518-3.el9.noarch 26/211 Verifying : readline-8.1-4.el9.ppc64le 27/211 Verifying : sed-4.8-9.el9.ppc64le 28/211 Verifying : xz-5.2.5-8.el9_0.ppc64le 29/211 Verifying : xz-libs-5.2.5-8.el9_0.ppc64le 30/211 Verifying : gzip-1.12-1.el9.ppc64le 31/211 Verifying : keyutils-libs-1.6.3-1.el9.ppc64le 32/211 Verifying : libpkgconf-1.7.3-10.el9.ppc64le 33/211 Verifying : pkgconf-1.7.3-10.el9.ppc64le 34/211 Verifying : pkgconf-m4-1.7.3-10.el9.noarch 35/211 Verifying : pkgconf-pkg-config-1.7.3-10.el9.ppc64le 36/211 Verifying : zip-3.0-35.el9.ppc64le 37/211 Verifying : gmp-1:6.2.0-13.el9.ppc64le 38/211 Verifying : libffi-3.4.2-8.el9.ppc64le 39/211 Verifying : lua-libs-5.4.4-4.el9.ppc64le 40/211 Verifying : zlib-1.2.11-40.el9.ppc64le 41/211 Verifying : bash-5.1.8-9.el9.ppc64le 42/211 Verifying : file-5.39-16.el9.ppc64le 43/211 Verifying : file-libs-5.39-16.el9.ppc64le 44/211 Verifying : libacl-2.3.1-4.el9.ppc64le 45/211 Verifying : setup-2.13.7-10.el9.noarch 46/211 Verifying : libevent-2.1.12-8.el9_4.ppc64le 47/211 Verifying : bzip2-1.0.8-10.el9_5.ppc64le 48/211 Verifying : bzip2-libs-1.0.8-10.el9_5.ppc64le 49/211 Verifying : filesystem-3.16-5.el9.ppc64le 50/211 Verifying : findutils-1:4.8.0-7.el9.ppc64le 51/211 Verifying : gdbm-libs-1:1.23-1.el9.ppc64le 52/211 Verifying : libbrotli-1.0.9-7.el9_5.ppc64le 53/211 Verifying : libeconf-0.4.1-4.el9.ppc64le 54/211 Verifying : libgcrypt-1.10.0-11.el9.ppc64le 55/211 Verifying : libnghttp2-1.43.0-6.el9.ppc64le 56/211 Verifying : librtas-2.0.6-1.el9.ppc64le 57/211 Verifying : p11-kit-0.25.3-3.el9_5.ppc64le 58/211 Verifying : p11-kit-trust-0.25.3-3.el9_5.ppc64le 59/211 Verifying : pcre-8.44-4.el9.ppc64le 60/211 Verifying : pcre2-10.40-6.el9.ppc64le 61/211 Verifying : pcre2-syntax-10.40-6.el9.noarch 62/211 Verifying : alternatives-1.24-2.el9.ppc64le 63/211 Verifying : coreutils-common-8.32-39.el9.ppc64le 64/211 Verifying : libfdisk-2.37.4-21.el9.ppc64le 65/211 Verifying : libmount-2.37.4-21.el9.ppc64le 66/211 Verifying : libselinux-3.6-3.el9.ppc64le 67/211 Verifying : libsemanage-3.6-5.el9_6.ppc64le 68/211 Verifying : libsmartcols-2.37.4-21.el9.ppc64le 69/211 Verifying : libtool-ltdl-2.4.6-46.el9.ppc64le 70/211 Verifying : libzstd-1.5.5-1.el9.ppc64le 71/211 Verifying : openldap-2.6.8-4.el9.ppc64le 72/211 Verifying : util-linux-2.37.4-21.el9.ppc64le 73/211 Verifying : util-linux-core-2.37.4-21.el9.ppc64le 74/211 Verifying : zstd-1.5.5-1.el9.ppc64le 75/211 Verifying : coreutils-8.32-39.el9.ppc64le 76/211 Verifying : krb5-libs-1.21.1-8.el9_6.ppc64le 77/211 Verifying : libblkid-2.37.4-21.el9.ppc64le 78/211 Verifying : libdb-5.3.28-57.el9_6.ppc64le 79/211 Verifying : libtasn1-4.16.0-9.el9.ppc64le 80/211 Verifying : libuuid-2.37.4-21.el9.ppc64le 81/211 Verifying : libarchive-3.5.3-6.el9_6.ppc64le 82/211 Verifying : pam-1.5.1-26.el9_6.ppc64le 83/211 Verifying : which-2.21-30.el9_6.ppc64le 84/211 Verifying : audit-libs-3.1.5-7.el9.ppc64le 85/211 Verifying : crypto-policies-20250905-1.git377cc42.el9_7.noar 86/211 Verifying : curl-7.76.1-34.el9.ppc64le 87/211 Verifying : cyrus-sasl-lib-2.1.27-22.el9.ppc64le 88/211 Verifying : elfutils-0.193-1.el9.ppc64le 89/211 Verifying : elfutils-debuginfod-client-0.193-1.el9.ppc64le 90/211 Verifying : elfutils-default-yama-scope-0.193-1.el9.noarch 91/211 Verifying : elfutils-libelf-0.193-1.el9.ppc64le 92/211 Verifying : elfutils-libs-0.193-1.el9.ppc64le 93/211 Verifying : libcap-2.48-10.el9.ppc64le 94/211 Verifying : libcom_err-1.46.5-8.el9.ppc64le 95/211 Verifying : libcurl-7.76.1-34.el9.ppc64le 96/211 Verifying : libgcc-11.5.0-11.el9.ppc64le 97/211 Verifying : libgomp-11.5.0-11.el9.ppc64le 98/211 Verifying : libsepol-3.6-3.el9.ppc64le 99/211 Verifying : libstdc++-11.5.0-11.el9.ppc64le 100/211 Verifying : ncurses-6.2-12.20210508.el9.ppc64le 101/211 Verifying : ncurses-base-6.2-12.20210508.el9.noarch 102/211 Verifying : ncurses-libs-6.2-12.20210508.el9.ppc64le 103/211 Verifying : openssl-fips-provider-3.0.7-8.el9.ppc64le 104/211 Verifying : openssl-fips-provider-so-3.0.7-8.el9.ppc64le 105/211 Verifying : rpm-4.16.1.3-39.el9.ppc64le 106/211 Verifying : rpm-build-libs-4.16.1.3-39.el9.ppc64le 107/211 Verifying : rpm-libs-4.16.1.3-39.el9.ppc64le 108/211 Verifying : shadow-utils-2:4.9-15.el9.ppc64le 109/211 Verifying : unzip-6.0-59.el9.ppc64le 110/211 Verifying : glibc-2.34-231.el9_7.2.ppc64le 111/211 Verifying : glibc-common-2.34-231.el9_7.2.ppc64le 112/211 Verifying : glibc-gconv-extra-2.34-231.el9_7.2.ppc64le 113/211 Verifying : glibc-minimal-langpack-2.34-231.el9_7.2.ppc64le 114/211 Verifying : redhat-release-9.7-0.7.el9.ppc64le 115/211 Verifying : sqlite-libs-3.34.1-9.el9_7.ppc64le 116/211 Verifying : ca-certificates-2025.2.80_v9.0.305-91.el9.noarch 117/211 Verifying : libxml2-2.9.13-14.el9_7.ppc64le 118/211 Verifying : systemd-libs-252-55.el9_7.7.ppc64le 119/211 Verifying : tzdata-2025c-1.el9.noarch 120/211 Verifying : libssh-0.10.4-17.el9_7.ppc64le 121/211 Verifying : libssh-config-0.10.4-17.el9_7.noarch 122/211 Verifying : binutils-2.35.2-67.el9_7.1.ppc64le 123/211 Verifying : binutils-gold-2.35.2-67.el9_7.1.ppc64le 124/211 Verifying : tar-2:1.34-9.el9_7.ppc64le 125/211 Verifying : openssl-1:3.5.1-5.el9_7.ppc64le 126/211 Verifying : openssl-libs-1:3.5.1-5.el9_7.ppc64le 127/211 Verifying : perl-Encode-4:3.08-462.el9.ppc64le 128/211 Verifying : perl-Exporter-5.74-461.el9.noarch 129/211 Verifying : perl-File-Temp-1:0.231.100-4.el9.noarch 130/211 Verifying : perl-MIME-Base64-3.16-4.el9.ppc64le 131/211 Verifying : perl-Mozilla-CA-20200520-6.el9.noarch 132/211 Verifying : perl-Socket-4:2.031-4.el9.ppc64le 133/211 Verifying : perl-Term-Cap-1.17-460.el9.noarch 134/211 Verifying : perl-Time-Local-2:1.300-7.el9.noarch 135/211 Verifying : perl-parent-1:0.238-460.el9.noarch 136/211 Verifying : perl-srpm-macros-1-41.el9.noarch 137/211 Verifying : rust-srpm-macros-17-4.el9.noarch 138/211 Verifying : ghc-srpm-macros-1.5.0-6.el9.noarch 139/211 Verifying : lua-srpm-macros-1-6.el9.noarch 140/211 Verifying : patch-2.7.6-16.el9.ppc64le 141/211 Verifying : perl-Digest-MD5-2.58-4.el9.ppc64le 142/211 Verifying : perl-IO-Socket-IP-0.41-5.el9.noarch 143/211 Verifying : perl-Pod-Escapes-1:1.07-460.el9.noarch 144/211 Verifying : perl-Pod-Simple-1:3.42-4.el9.noarch 145/211 Verifying : perl-Term-ANSIColor-5.01-461.el9.noarch 146/211 Verifying : perl-Text-ParseWords-3.30-460.el9.noarch 147/211 Verifying : perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch 148/211 Verifying : perl-URI-5.09-3.el9.noarch 149/211 Verifying : perl-constant-1.33-461.el9.noarch 150/211 Verifying : openblas-srpm-macros-2-11.el9.noarch 151/211 Verifying : perl-Data-Dumper-2.174-462.el9.ppc64le 152/211 Verifying : perl-File-Path-2.18-4.el9.noarch 153/211 Verifying : perl-Pod-Perldoc-3.28.01-461.el9.noarch 154/211 Verifying : perl-Pod-Usage-4:2.01-4.el9.noarch 155/211 Verifying : perl-libnet-3.13-4.el9.noarch 156/211 Verifying : perl-podlators-1:4.14-460.el9.noarch 157/211 Verifying : fonts-srpm-macros-1:2.0.5-7.el9.1.noarch 158/211 Verifying : ocaml-srpm-macros-6-6.el9.noarch 159/211 Verifying : perl-Carp-1.50-460.el9.noarch 160/211 Verifying : perl-Digest-1.19-4.el9.noarch 161/211 Verifying : perl-Getopt-Long-1:2.52-4.el9.noarch 162/211 Verifying : perl-Storable-1:3.21-460.el9.ppc64le 163/211 Verifying : perl-PathTools-3.78-461.el9.ppc64le 164/211 Verifying : qt5-srpm-macros-5.15.9-1.el9.noarch 165/211 Verifying : perl-HTTP-Tiny-0.076-462.el9.noarch 166/211 Verifying : perl-Scalar-List-Utils-4:1.56-462.el9.ppc64le 167/211 Verifying : perl-IO-Socket-SSL-2.073-2.el9.noarch 168/211 Verifying : python-srpm-macros-3.9-54.el9.noarch 169/211 Verifying : pyproject-srpm-macros-1.16.2-1.el9.noarch 170/211 Verifying : perl-AutoLoader-5.74-481.1.el9_6.noarch 171/211 Verifying : perl-B-1.80-481.1.el9_6.ppc64le 172/211 Verifying : perl-Class-Struct-0.66-481.1.el9_6.noarch 173/211 Verifying : perl-Errno-1.30-481.1.el9_6.ppc64le 174/211 Verifying : perl-Fcntl-1.13-481.1.el9_6.ppc64le 175/211 Verifying : perl-File-Basename-2.85-481.1.el9_6.noarch 176/211 Verifying : perl-File-stat-1.09-481.1.el9_6.noarch 177/211 Verifying : perl-FileHandle-2.03-481.1.el9_6.noarch 178/211 Verifying : perl-Getopt-Std-1.12-481.1.el9_6.noarch 179/211 Verifying : perl-IO-1.43-481.1.el9_6.ppc64le 180/211 Verifying : perl-IPC-Open3-1.21-481.1.el9_6.noarch 181/211 Verifying : perl-POSIX-1.94-481.1.el9_6.ppc64le 182/211 Verifying : perl-SelectSaver-1.02-481.1.el9_6.noarch 183/211 Verifying : perl-Symbol-1.08-481.1.el9_6.noarch 184/211 Verifying : perl-base-2.27-481.1.el9_6.noarch 185/211 Verifying : perl-if-0.60.800-481.1.el9_6.noarch 186/211 Verifying : perl-interpreter-4:5.32.1-481.1.el9_6.ppc64le 187/211 Verifying : perl-libs-4:5.32.1-481.1.el9_6.ppc64le 188/211 Verifying : perl-mro-1.23-481.1.el9_6.ppc64le 189/211 Verifying : perl-overload-1.31-481.1.el9_6.noarch 190/211 Verifying : perl-overloading-0.02-481.1.el9_6.noarch 191/211 Verifying : perl-subs-1.03-481.1.el9_6.noarch 192/211 Verifying : perl-vars-1.05-481.1.el9_6.noarch 193/211 Verifying : efi-srpm-macros-6-4.el9.noarch 194/211 Verifying : gdb-minimal-16.3-2.el9.ppc64le 195/211 Verifying : redhat-rpm-config-210-1.el9.noarch 196/211 Verifying : rpm-build-4.16.1.3-39.el9.ppc64le 197/211 Verifying : debugedit-5.0-11.el9.ppc64le 198/211 Verifying : dwz-0.16-1.el9.ppc64le 199/211 Verifying : kernel-srpm-macros-1.0-14.el9.noarch 200/211 Verifying : perl-Net-SSLeay-1.94-3.el9.ppc64le 201/211 Verifying : go-srpm-macros-3.6.0-12.el9_7.noarch 202/211 Verifying : ansible-srpm-macros-1-16.el9.noarch 203/211 Verifying : epel-rpm-macros-9-17.el9.noarch 204/211 Verifying : forge-srpm-macros-0.4.0-1.el9.noarch 205/211 Verifying : fpc-srpm-macros-1.3-7.el9.noarch 206/211 Verifying : ghc-srpm-macros-epel-1.9.1-1.el9.noarch 207/211 Verifying : go-srpm-macros-epel-3.8.0-1.el9.noarch 208/211 Verifying : qt6-srpm-macros-6.6.2-1.el9.noarch 209/211 Verifying : rpmautospec-rpm-macros-0.8.1-11.el9.noarch 210/211 Verifying : rust-srpm-macros-epel-26.3-1.el9.noarch 211/211 Installed products updated. Installed: alternatives-1.24-2.el9.ppc64le ansible-srpm-macros-1-16.el9.noarch audit-libs-3.1.5-7.el9.ppc64le basesystem-11-13.el9.noarch bash-5.1.8-9.el9.ppc64le binutils-2.35.2-67.el9_7.1.ppc64le binutils-gold-2.35.2-67.el9_7.1.ppc64le bzip2-1.0.8-10.el9_5.ppc64le bzip2-libs-1.0.8-10.el9_5.ppc64le ca-certificates-2025.2.80_v9.0.305-91.el9.noarch coreutils-8.32-39.el9.ppc64le coreutils-common-8.32-39.el9.ppc64le cpio-2.13-16.el9.ppc64le cracklib-2.9.6-27.el9.ppc64le cracklib-dicts-2.9.6-27.el9.ppc64le crypto-policies-20250905-1.git377cc42.el9_7.noarch curl-7.76.1-34.el9.ppc64le cyrus-sasl-lib-2.1.27-22.el9.ppc64le debugedit-5.0-11.el9.ppc64le diffutils-3.7-12.el9.ppc64le dwz-0.16-1.el9.ppc64le ed-1.14.2-12.el9.ppc64le efi-srpm-macros-6-4.el9.noarch elfutils-0.193-1.el9.ppc64le elfutils-debuginfod-client-0.193-1.el9.ppc64le elfutils-default-yama-scope-0.193-1.el9.noarch elfutils-libelf-0.193-1.el9.ppc64le elfutils-libs-0.193-1.el9.ppc64le epel-rpm-macros-9-17.el9.noarch file-5.39-16.el9.ppc64le file-libs-5.39-16.el9.ppc64le filesystem-3.16-5.el9.ppc64le findutils-1:4.8.0-7.el9.ppc64le fonts-srpm-macros-1:2.0.5-7.el9.1.noarch forge-srpm-macros-0.4.0-1.el9.noarch fpc-srpm-macros-1.3-7.el9.noarch gawk-5.1.0-6.el9.ppc64le gdb-minimal-16.3-2.el9.ppc64le gdbm-libs-1:1.23-1.el9.ppc64le ghc-srpm-macros-1.5.0-6.el9.noarch ghc-srpm-macros-epel-1.9.1-1.el9.noarch glibc-2.34-231.el9_7.2.ppc64le glibc-common-2.34-231.el9_7.2.ppc64le glibc-gconv-extra-2.34-231.el9_7.2.ppc64le glibc-minimal-langpack-2.34-231.el9_7.2.ppc64le gmp-1:6.2.0-13.el9.ppc64le go-srpm-macros-3.6.0-12.el9_7.noarch go-srpm-macros-epel-3.8.0-1.el9.noarch grep-3.6-5.el9.ppc64le groff-base-1.22.4-10.el9.ppc64le gzip-1.12-1.el9.ppc64le info-6.7-15.el9.ppc64le json-c-0.14-11.el9.ppc64le kernel-srpm-macros-1.0-14.el9.noarch keyutils-libs-1.6.3-1.el9.ppc64le krb5-libs-1.21.1-8.el9_6.ppc64le libacl-2.3.1-4.el9.ppc64le libarchive-3.5.3-6.el9_6.ppc64le libattr-2.5.1-3.el9.ppc64le libblkid-2.37.4-21.el9.ppc64le libbrotli-1.0.9-7.el9_5.ppc64le libcap-2.48-10.el9.ppc64le libcap-ng-0.8.2-7.el9.ppc64le libcom_err-1.46.5-8.el9.ppc64le libcurl-7.76.1-34.el9.ppc64le libdb-5.3.28-57.el9_6.ppc64le libeconf-0.4.1-4.el9.ppc64le libevent-2.1.12-8.el9_4.ppc64le libfdisk-2.37.4-21.el9.ppc64le libffi-3.4.2-8.el9.ppc64le libgcc-11.5.0-11.el9.ppc64le libgcrypt-1.10.0-11.el9.ppc64le libgomp-11.5.0-11.el9.ppc64le libgpg-error-1.42-5.el9.ppc64le libidn2-2.3.0-7.el9.ppc64le libmount-2.37.4-21.el9.ppc64le libnghttp2-1.43.0-6.el9.ppc64le libpkgconf-1.7.3-10.el9.ppc64le libpsl-0.21.1-5.el9.ppc64le libpwquality-1.4.4-8.el9.ppc64le librtas-2.0.6-1.el9.ppc64le libselinux-3.6-3.el9.ppc64le libsemanage-3.6-5.el9_6.ppc64le libsepol-3.6-3.el9.ppc64le libsigsegv-2.13-4.el9.ppc64le libsmartcols-2.37.4-21.el9.ppc64le libssh-0.10.4-17.el9_7.ppc64le libssh-config-0.10.4-17.el9_7.noarch libstdc++-11.5.0-11.el9.ppc64le libtasn1-4.16.0-9.el9.ppc64le libtool-ltdl-2.4.6-46.el9.ppc64le libunistring-0.9.10-15.el9.ppc64le libutempter-1.2.1-6.el9.ppc64le libuuid-2.37.4-21.el9.ppc64le libverto-0.3.2-3.el9.ppc64le libxcrypt-4.4.18-3.el9.ppc64le libxml2-2.9.13-14.el9_7.ppc64le libzstd-1.5.5-1.el9.ppc64le lua-libs-5.4.4-4.el9.ppc64le lua-srpm-macros-1-6.el9.noarch lz4-libs-1.9.3-5.el9.ppc64le mpfr-4.1.0-7.el9.ppc64le ncurses-6.2-12.20210508.el9.ppc64le ncurses-base-6.2-12.20210508.el9.noarch ncurses-libs-6.2-12.20210508.el9.ppc64le ocaml-srpm-macros-6-6.el9.noarch openblas-srpm-macros-2-11.el9.noarch openldap-2.6.8-4.el9.ppc64le openssl-1:3.5.1-5.el9_7.ppc64le openssl-fips-provider-3.0.7-8.el9.ppc64le openssl-fips-provider-so-3.0.7-8.el9.ppc64le openssl-libs-1:3.5.1-5.el9_7.ppc64le p11-kit-0.25.3-3.el9_5.ppc64le p11-kit-trust-0.25.3-3.el9_5.ppc64le pam-1.5.1-26.el9_6.ppc64le patch-2.7.6-16.el9.ppc64le pcre-8.44-4.el9.ppc64le pcre2-10.40-6.el9.ppc64le pcre2-syntax-10.40-6.el9.noarch perl-AutoLoader-5.74-481.1.el9_6.noarch perl-B-1.80-481.1.el9_6.ppc64le perl-Carp-1.50-460.el9.noarch perl-Class-Struct-0.66-481.1.el9_6.noarch perl-Data-Dumper-2.174-462.el9.ppc64le perl-Digest-1.19-4.el9.noarch perl-Digest-MD5-2.58-4.el9.ppc64le perl-Encode-4:3.08-462.el9.ppc64le perl-Errno-1.30-481.1.el9_6.ppc64le perl-Exporter-5.74-461.el9.noarch perl-Fcntl-1.13-481.1.el9_6.ppc64le perl-File-Basename-2.85-481.1.el9_6.noarch perl-File-Path-2.18-4.el9.noarch perl-File-Temp-1:0.231.100-4.el9.noarch perl-File-stat-1.09-481.1.el9_6.noarch perl-FileHandle-2.03-481.1.el9_6.noarch perl-Getopt-Long-1:2.52-4.el9.noarch perl-Getopt-Std-1.12-481.1.el9_6.noarch perl-HTTP-Tiny-0.076-462.el9.noarch perl-IO-1.43-481.1.el9_6.ppc64le perl-IO-Socket-IP-0.41-5.el9.noarch perl-IO-Socket-SSL-2.073-2.el9.noarch perl-IPC-Open3-1.21-481.1.el9_6.noarch perl-MIME-Base64-3.16-4.el9.ppc64le perl-Mozilla-CA-20200520-6.el9.noarch perl-Net-SSLeay-1.94-3.el9.ppc64le perl-POSIX-1.94-481.1.el9_6.ppc64le perl-PathTools-3.78-461.el9.ppc64le perl-Pod-Escapes-1:1.07-460.el9.noarch perl-Pod-Perldoc-3.28.01-461.el9.noarch perl-Pod-Simple-1:3.42-4.el9.noarch perl-Pod-Usage-4:2.01-4.el9.noarch perl-Scalar-List-Utils-4:1.56-462.el9.ppc64le perl-SelectSaver-1.02-481.1.el9_6.noarch perl-Socket-4:2.031-4.el9.ppc64le perl-Storable-1:3.21-460.el9.ppc64le perl-Symbol-1.08-481.1.el9_6.noarch perl-Term-ANSIColor-5.01-461.el9.noarch perl-Term-Cap-1.17-460.el9.noarch perl-Text-ParseWords-3.30-460.el9.noarch perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch perl-Time-Local-2:1.300-7.el9.noarch perl-URI-5.09-3.el9.noarch perl-base-2.27-481.1.el9_6.noarch perl-constant-1.33-461.el9.noarch perl-if-0.60.800-481.1.el9_6.noarch perl-interpreter-4:5.32.1-481.1.el9_6.ppc64le perl-libnet-3.13-4.el9.noarch perl-libs-4:5.32.1-481.1.el9_6.ppc64le perl-mro-1.23-481.1.el9_6.ppc64le perl-overload-1.31-481.1.el9_6.noarch perl-overloading-0.02-481.1.el9_6.noarch perl-parent-1:0.238-460.el9.noarch perl-podlators-1:4.14-460.el9.noarch perl-srpm-macros-1-41.el9.noarch perl-subs-1.03-481.1.el9_6.noarch perl-vars-1.05-481.1.el9_6.noarch pkgconf-1.7.3-10.el9.ppc64le pkgconf-m4-1.7.3-10.el9.noarch pkgconf-pkg-config-1.7.3-10.el9.ppc64le popt-1.18-8.el9.ppc64le publicsuffix-list-dafsa-20210518-3.el9.noarch pyproject-srpm-macros-1.16.2-1.el9.noarch python-srpm-macros-3.9-54.el9.noarch qt5-srpm-macros-5.15.9-1.el9.noarch qt6-srpm-macros-6.6.2-1.el9.noarch readline-8.1-4.el9.ppc64le redhat-release-9.7-0.7.el9.ppc64le redhat-rpm-config-210-1.el9.noarch rpm-4.16.1.3-39.el9.ppc64le rpm-build-4.16.1.3-39.el9.ppc64le rpm-build-libs-4.16.1.3-39.el9.ppc64le rpm-libs-4.16.1.3-39.el9.ppc64le rpmautospec-rpm-macros-0.8.1-11.el9.noarch rust-srpm-macros-17-4.el9.noarch rust-srpm-macros-epel-26.3-1.el9.noarch sed-4.8-9.el9.ppc64le setup-2.13.7-10.el9.noarch shadow-utils-2:4.9-15.el9.ppc64le sqlite-libs-3.34.1-9.el9_7.ppc64le systemd-libs-252-55.el9_7.7.ppc64le tar-2:1.34-9.el9_7.ppc64le tzdata-2025c-1.el9.noarch unzip-6.0-59.el9.ppc64le util-linux-2.37.4-21.el9.ppc64le util-linux-core-2.37.4-21.el9.ppc64le which-2.21-30.el9_6.ppc64le xz-5.2.5-8.el9_0.ppc64le xz-libs-5.2.5-8.el9_0.ppc64le zip-3.0-35.el9.ppc64le zlib-1.2.11-40.el9.ppc64le zstd-1.5.5-1.el9.ppc64le Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.24-2.el9.ppc64le ansible-srpm-macros-1-16.el9.noarch audit-libs-3.1.5-7.el9.ppc64le basesystem-11-13.el9.noarch bash-5.1.8-9.el9.ppc64le binutils-2.35.2-67.el9_7.1.ppc64le binutils-gold-2.35.2-67.el9_7.1.ppc64le bzip2-1.0.8-10.el9_5.ppc64le bzip2-libs-1.0.8-10.el9_5.ppc64le ca-certificates-2025.2.80_v9.0.305-91.el9.noarch coreutils-8.32-39.el9.ppc64le coreutils-common-8.32-39.el9.ppc64le cpio-2.13-16.el9.ppc64le cracklib-2.9.6-27.el9.ppc64le cracklib-dicts-2.9.6-27.el9.ppc64le crypto-policies-20250905-1.git377cc42.el9_7.noarch curl-7.76.1-34.el9.ppc64le cyrus-sasl-lib-2.1.27-22.el9.ppc64le debugedit-5.0-11.el9.ppc64le diffutils-3.7-12.el9.ppc64le dwz-0.16-1.el9.ppc64le ed-1.14.2-12.el9.ppc64le efi-srpm-macros-6-4.el9.noarch elfutils-0.193-1.el9.ppc64le elfutils-debuginfod-client-0.193-1.el9.ppc64le elfutils-default-yama-scope-0.193-1.el9.noarch elfutils-libelf-0.193-1.el9.ppc64le elfutils-libs-0.193-1.el9.ppc64le epel-rpm-macros-9-17.el9.noarch file-5.39-16.el9.ppc64le file-libs-5.39-16.el9.ppc64le filesystem-3.16-5.el9.ppc64le findutils-4.8.0-7.el9.ppc64le fonts-srpm-macros-2.0.5-7.el9.1.noarch forge-srpm-macros-0.4.0-1.el9.noarch fpc-srpm-macros-1.3-7.el9.noarch gawk-5.1.0-6.el9.ppc64le gdb-minimal-16.3-2.el9.ppc64le gdbm-libs-1.23-1.el9.ppc64le ghc-srpm-macros-1.5.0-6.el9.noarch ghc-srpm-macros-epel-1.9.1-1.el9.noarch glibc-2.34-231.el9_7.2.ppc64le glibc-common-2.34-231.el9_7.2.ppc64le glibc-gconv-extra-2.34-231.el9_7.2.ppc64le glibc-minimal-langpack-2.34-231.el9_7.2.ppc64le gmp-6.2.0-13.el9.ppc64le go-srpm-macros-3.6.0-12.el9_7.noarch go-srpm-macros-epel-3.8.0-1.el9.noarch gpg-pubkey-3228467c-613798eb gpg-pubkey-5a6340b3-6229229e gpg-pubkey-fd431d51-4ae0493b grep-3.6-5.el9.ppc64le groff-base-1.22.4-10.el9.ppc64le gzip-1.12-1.el9.ppc64le info-6.7-15.el9.ppc64le json-c-0.14-11.el9.ppc64le kernel-srpm-macros-1.0-14.el9.noarch keyutils-libs-1.6.3-1.el9.ppc64le krb5-libs-1.21.1-8.el9_6.ppc64le libacl-2.3.1-4.el9.ppc64le libarchive-3.5.3-6.el9_6.ppc64le libattr-2.5.1-3.el9.ppc64le libblkid-2.37.4-21.el9.ppc64le libbrotli-1.0.9-7.el9_5.ppc64le libcap-2.48-10.el9.ppc64le libcap-ng-0.8.2-7.el9.ppc64le libcom_err-1.46.5-8.el9.ppc64le libcurl-7.76.1-34.el9.ppc64le libdb-5.3.28-57.el9_6.ppc64le libeconf-0.4.1-4.el9.ppc64le libevent-2.1.12-8.el9_4.ppc64le libfdisk-2.37.4-21.el9.ppc64le libffi-3.4.2-8.el9.ppc64le libgcc-11.5.0-11.el9.ppc64le libgcrypt-1.10.0-11.el9.ppc64le libgomp-11.5.0-11.el9.ppc64le libgpg-error-1.42-5.el9.ppc64le libidn2-2.3.0-7.el9.ppc64le libmount-2.37.4-21.el9.ppc64le libnghttp2-1.43.0-6.el9.ppc64le libpkgconf-1.7.3-10.el9.ppc64le libpsl-0.21.1-5.el9.ppc64le libpwquality-1.4.4-8.el9.ppc64le librtas-2.0.6-1.el9.ppc64le libselinux-3.6-3.el9.ppc64le libsemanage-3.6-5.el9_6.ppc64le libsepol-3.6-3.el9.ppc64le libsigsegv-2.13-4.el9.ppc64le libsmartcols-2.37.4-21.el9.ppc64le libssh-0.10.4-17.el9_7.ppc64le libssh-config-0.10.4-17.el9_7.noarch libstdc++-11.5.0-11.el9.ppc64le libtasn1-4.16.0-9.el9.ppc64le libtool-ltdl-2.4.6-46.el9.ppc64le libunistring-0.9.10-15.el9.ppc64le libutempter-1.2.1-6.el9.ppc64le libuuid-2.37.4-21.el9.ppc64le libverto-0.3.2-3.el9.ppc64le libxcrypt-4.4.18-3.el9.ppc64le libxml2-2.9.13-14.el9_7.ppc64le libzstd-1.5.5-1.el9.ppc64le lua-libs-5.4.4-4.el9.ppc64le lua-srpm-macros-1-6.el9.noarch lz4-libs-1.9.3-5.el9.ppc64le mpfr-4.1.0-7.el9.ppc64le ncurses-6.2-12.20210508.el9.ppc64le ncurses-base-6.2-12.20210508.el9.noarch ncurses-libs-6.2-12.20210508.el9.ppc64le ocaml-srpm-macros-6-6.el9.noarch openblas-srpm-macros-2-11.el9.noarch openldap-2.6.8-4.el9.ppc64le openssl-3.5.1-5.el9_7.ppc64le openssl-fips-provider-3.0.7-8.el9.ppc64le openssl-fips-provider-so-3.0.7-8.el9.ppc64le openssl-libs-3.5.1-5.el9_7.ppc64le p11-kit-0.25.3-3.el9_5.ppc64le p11-kit-trust-0.25.3-3.el9_5.ppc64le pam-1.5.1-26.el9_6.ppc64le patch-2.7.6-16.el9.ppc64le pcre-8.44-4.el9.ppc64le pcre2-10.40-6.el9.ppc64le pcre2-syntax-10.40-6.el9.noarch perl-AutoLoader-5.74-481.1.el9_6.noarch perl-B-1.80-481.1.el9_6.ppc64le perl-Carp-1.50-460.el9.noarch perl-Class-Struct-0.66-481.1.el9_6.noarch perl-Data-Dumper-2.174-462.el9.ppc64le perl-Digest-1.19-4.el9.noarch perl-Digest-MD5-2.58-4.el9.ppc64le perl-Encode-3.08-462.el9.ppc64le perl-Errno-1.30-481.1.el9_6.ppc64le perl-Exporter-5.74-461.el9.noarch perl-Fcntl-1.13-481.1.el9_6.ppc64le perl-File-Basename-2.85-481.1.el9_6.noarch perl-File-Path-2.18-4.el9.noarch perl-File-Temp-0.231.100-4.el9.noarch perl-File-stat-1.09-481.1.el9_6.noarch perl-FileHandle-2.03-481.1.el9_6.noarch perl-Getopt-Long-2.52-4.el9.noarch perl-Getopt-Std-1.12-481.1.el9_6.noarch perl-HTTP-Tiny-0.076-462.el9.noarch perl-IO-1.43-481.1.el9_6.ppc64le perl-IO-Socket-IP-0.41-5.el9.noarch perl-IO-Socket-SSL-2.073-2.el9.noarch perl-IPC-Open3-1.21-481.1.el9_6.noarch perl-MIME-Base64-3.16-4.el9.ppc64le perl-Mozilla-CA-20200520-6.el9.noarch perl-Net-SSLeay-1.94-3.el9.ppc64le perl-POSIX-1.94-481.1.el9_6.ppc64le perl-PathTools-3.78-461.el9.ppc64le perl-Pod-Escapes-1.07-460.el9.noarch perl-Pod-Perldoc-3.28.01-461.el9.noarch perl-Pod-Simple-3.42-4.el9.noarch perl-Pod-Usage-2.01-4.el9.noarch perl-Scalar-List-Utils-1.56-462.el9.ppc64le perl-SelectSaver-1.02-481.1.el9_6.noarch perl-Socket-2.031-4.el9.ppc64le perl-Storable-3.21-460.el9.ppc64le perl-Symbol-1.08-481.1.el9_6.noarch perl-Term-ANSIColor-5.01-461.el9.noarch perl-Term-Cap-1.17-460.el9.noarch perl-Text-ParseWords-3.30-460.el9.noarch perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch perl-Time-Local-1.300-7.el9.noarch perl-URI-5.09-3.el9.noarch perl-base-2.27-481.1.el9_6.noarch perl-constant-1.33-461.el9.noarch perl-if-0.60.800-481.1.el9_6.noarch perl-interpreter-5.32.1-481.1.el9_6.ppc64le perl-libnet-3.13-4.el9.noarch perl-libs-5.32.1-481.1.el9_6.ppc64le perl-mro-1.23-481.1.el9_6.ppc64le perl-overload-1.31-481.1.el9_6.noarch perl-overloading-0.02-481.1.el9_6.noarch perl-parent-0.238-460.el9.noarch perl-podlators-4.14-460.el9.noarch perl-srpm-macros-1-41.el9.noarch perl-subs-1.03-481.1.el9_6.noarch perl-vars-1.05-481.1.el9_6.noarch pkgconf-1.7.3-10.el9.ppc64le pkgconf-m4-1.7.3-10.el9.noarch pkgconf-pkg-config-1.7.3-10.el9.ppc64le popt-1.18-8.el9.ppc64le publicsuffix-list-dafsa-20210518-3.el9.noarch pyproject-srpm-macros-1.16.2-1.el9.noarch python-srpm-macros-3.9-54.el9.noarch qt5-srpm-macros-5.15.9-1.el9.noarch qt6-srpm-macros-6.6.2-1.el9.noarch readline-8.1-4.el9.ppc64le redhat-release-9.7-0.7.el9.ppc64le redhat-rpm-config-210-1.el9.noarch rpm-4.16.1.3-39.el9.ppc64le rpm-build-4.16.1.3-39.el9.ppc64le rpm-build-libs-4.16.1.3-39.el9.ppc64le rpm-libs-4.16.1.3-39.el9.ppc64le rpmautospec-rpm-macros-0.8.1-11.el9.noarch rust-srpm-macros-17-4.el9.noarch rust-srpm-macros-epel-26.3-1.el9.noarch sed-4.8-9.el9.ppc64le setup-2.13.7-10.el9.noarch shadow-utils-4.9-15.el9.ppc64le sqlite-libs-3.34.1-9.el9_7.ppc64le systemd-libs-252-55.el9_7.7.ppc64le tar-1.34-9.el9_7.ppc64le tzdata-2025c-1.el9.noarch unzip-6.0-59.el9.ppc64le util-linux-2.37.4-21.el9.ppc64le util-linux-core-2.37.4-21.el9.ppc64le which-2.21-30.el9_6.ppc64le xz-5.2.5-8.el9_0.ppc64le xz-libs-5.2.5-8.el9_0.ppc64le zip-3.0-35.el9.ppc64le zlib-1.2.11-40.el9.ppc64le zstd-1.5.5-1.el9.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.el9.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-9-ppc64le-1769509438.093451/root/var/log/dnf.rpm.log /var/lib/mock/rhel+epel-9-ppc64le-1769509438.093451/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-9-ppc64le-1769509438.093451/root/var/log/dnf.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-rl974j4p/samtools/samtools.spec) Config(child) 3 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 INFO: Start(/var/lib/copr-rpmbuild/results/samtools-1.23-1.el9.src.rpm) Config(rhel+epel-9-ppc64le) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-ppc64le-bootstrap-1769509438.093451/root. INFO: reusing tmpfs at /var/lib/mock/rhel+epel-9-ppc64le-bootstrap-1769509438.093451/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-ppc64le-1769509438.093451/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.16.1.3-39.el9.ppc64le python3-dnf-4.14.0-31.el9.noarch python3-dnf-plugins-core-4.3.0-24.el9_7.noarch yum-4.14.0-31.el9.noarch Finish: chroot init Start: build phase for samtools-1.23-1.el9.src.rpm Start: build setup for samtools-1.23-1.el9.src.rpm Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1769040000 Wrote: /builddir/build/SRPMS/samtools-1.23-1.el9.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 7.3 kB/s | 1.5 kB 00:00 Copr repository 6.2 kB/s | 10 kB 00:01 Red Hat Enterprise Linux - BaseOS 7.0 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux - AppStream 13 kB/s | 4.5 kB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 35 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 9 - ppc64le 594 kB/s | 23 kB 00:00 Package perl-Getopt-Long-1:2.52-4.el9.noarch is already installed. Package perl-interpreter-4:5.32.1-481.1.el9_6.ppc64le is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: gcc ppc64le 11.5.0-11.el9 appstream 28 M htslib-devel ppc64le 1.23-1.el9 copr_base 107 k htslib-tools ppc64le 1.23-1.el9 copr_base 800 k make ppc64le 1:4.3-8.el9 baseos 554 k ncurses-devel ppc64le 6.2-12.20210508.el9 appstream 728 k perl-FindBin noarch 1.51-481.1.el9_6 appstream 14 k perl-lib ppc64le 0.65-481.1.el9_6 appstream 14 k zlib-devel ppc64le 1.2.11-40.el9 appstream 47 k Installing dependencies: annobin ppc64le 12.98-1.el9 appstream 1.1 M cpp ppc64le 11.5.0-11.el9 appstream 9.2 M gcc-plugin-annobin ppc64le 11.5.0-11.el9 appstream 39 k glibc-devel ppc64le 2.34-231.el9_7.2 appstream 569 k htslib ppc64le 1.23-1.el9 copr_base 622 k kernel-headers ppc64le 5.14.0-611.26.1.el9_7 appstream 2.9 M libasan ppc64le 11.5.0-11.el9 appstream 430 k libatomic ppc64le 11.5.0-11.el9 baseos 24 k libedit ppc64le 3.1-38.20210216cvs.el9 baseos 119 k libmpc ppc64le 1.2.1-4.el9 appstream 70 k libubsan ppc64le 11.5.0-11.el9 appstream 197 k libxcrypt-devel ppc64le 4.4.18-3.el9 appstream 32 k llvm-filesystem ppc64le 20.1.8-3.el9 appstream 9.1 k llvm-libs ppc64le 20.1.8-3.el9 appstream 30 M ncurses-c++-libs ppc64le 6.2-12.20210508.el9 appstream 38 k Transaction Summary ================================================================================ Install 23 Packages Total download size: 75 M Installed size: 259 M Downloading Packages: (1/23): htslib-devel-1.23-1.el9.ppc64le.rpm 437 kB/s | 107 kB 00:00 (2/23): htslib-1.23-1.el9.ppc64le.rpm 1.8 MB/s | 622 kB 00:00 (3/23): libedit-3.1-38.20210216cvs.el9.ppc64le. 699 kB/s | 119 kB 00:00 (4/23): make-4.3-8.el9.ppc64le.rpm 3.1 MB/s | 554 kB 00:00 (5/23): libatomic-11.5.0-11.el9.ppc64le.rpm 276 kB/s | 24 kB 00:00 (6/23): htslib-tools-1.23-1.el9.ppc64le.rpm 1.4 MB/s | 800 kB 00:00 (7/23): libmpc-1.2.1-4.el9.ppc64le.rpm 811 kB/s | 70 kB 00:00 (8/23): libxcrypt-devel-4.4.18-3.el9.ppc64le.rp 342 kB/s | 32 kB 00:00 (9/23): perl-FindBin-1.51-481.1.el9_6.noarch.rp 161 kB/s | 14 kB 00:00 (10/23): zlib-devel-1.2.11-40.el9.ppc64le.rpm 327 kB/s | 47 kB 00:00 (11/23): perl-lib-0.65-481.1.el9_6.ppc64le.rpm 166 kB/s | 14 kB 00:00 (12/23): gcc-plugin-annobin-11.5.0-11.el9.ppc64 459 kB/s | 39 kB 00:00 (13/23): cpp-11.5.0-11.el9.ppc64le.rpm 32 MB/s | 9.2 MB 00:00 (14/23): annobin-12.98-1.el9.ppc64le.rpm 5.9 MB/s | 1.1 MB 00:00 (15/23): libasan-11.5.0-11.el9.ppc64le.rpm 3.8 MB/s | 430 kB 00:00 (16/23): libubsan-11.5.0-11.el9.ppc64le.rpm 2.0 MB/s | 197 kB 00:00 (17/23): llvm-filesystem-20.1.8-3.el9.ppc64le.r 105 kB/s | 9.1 kB 00:00 (18/23): llvm-libs-20.1.8-3.el9.ppc64le.rpm 41 MB/s | 30 MB 00:00 (19/23): ncurses-c++-libs-6.2-12.20210508.el9.p 229 kB/s | 38 kB 00:00 (20/23): glibc-devel-2.34-231.el9_7.2.ppc64le.r 5.8 MB/s | 569 kB 00:00 (21/23): ncurses-devel-6.2-12.20210508.el9.ppc6 6.2 MB/s | 728 kB 00:00 (22/23): gcc-11.5.0-11.el9.ppc64le.rpm 38 MB/s | 28 MB 00:00 (23/23): kernel-headers-5.14.0-611.26.1.el9_7.p 16 MB/s | 2.9 MB 00:00 -------------------------------------------------------------------------------- Total 43 MB/s | 75 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-4.el9.ppc64le 1/23 Installing : htslib-1.23-1.el9.ppc64le 2/23 Installing : cpp-11.5.0-11.el9.ppc64le 3/23 Installing : kernel-headers-5.14.0-611.26.1.el9_7.ppc64le 4/23 Installing : glibc-devel-2.34-231.el9_7.2.ppc64le 5/23 Installing : libxcrypt-devel-4.4.18-3.el9.ppc64le 6/23 Installing : ncurses-c++-libs-6.2-12.20210508.el9.ppc64le 7/23 Installing : llvm-filesystem-20.1.8-3.el9.ppc64le 8/23 Installing : libubsan-11.5.0-11.el9.ppc64le 9/23 Installing : libasan-11.5.0-11.el9.ppc64le 10/23 Installing : libatomic-11.5.0-11.el9.ppc64le 11/23 Installing : make-1:4.3-8.el9.ppc64le 12/23 Installing : gcc-11.5.0-11.el9.ppc64le 13/23 Running scriptlet: gcc-11.5.0-11.el9.ppc64le 13/23 Installing : libedit-3.1-38.20210216cvs.el9.ppc64le 14/23 Installing : llvm-libs-20.1.8-3.el9.ppc64le 15/23 Installing : annobin-12.98-1.el9.ppc64le 16/23 Running scriptlet: annobin-12.98-1.el9.ppc64le 16/23 Installing : gcc-plugin-annobin-11.5.0-11.el9.ppc64le 17/23 Running scriptlet: gcc-plugin-annobin-11.5.0-11.el9.ppc64le 17/23 Installing : ncurses-devel-6.2-12.20210508.el9.ppc64le 18/23 Installing : htslib-devel-1.23-1.el9.ppc64le 19/23 Installing : htslib-tools-1.23-1.el9.ppc64le 20/23 Installing : perl-lib-0.65-481.1.el9_6.ppc64le 21/23 Installing : perl-FindBin-1.51-481.1.el9_6.noarch 22/23 Installing : zlib-devel-1.2.11-40.el9.ppc64le 23/23 Running scriptlet: zlib-devel-1.2.11-40.el9.ppc64le 23/23 Verifying : htslib-1.23-1.el9.ppc64le 1/23 Verifying : htslib-devel-1.23-1.el9.ppc64le 2/23 Verifying : htslib-tools-1.23-1.el9.ppc64le 3/23 Verifying : libedit-3.1-38.20210216cvs.el9.ppc64le 4/23 Verifying : make-1:4.3-8.el9.ppc64le 5/23 Verifying : libatomic-11.5.0-11.el9.ppc64le 6/23 Verifying : libmpc-1.2.1-4.el9.ppc64le 7/23 Verifying : libxcrypt-devel-4.4.18-3.el9.ppc64le 8/23 Verifying : zlib-devel-1.2.11-40.el9.ppc64le 9/23 Verifying : perl-FindBin-1.51-481.1.el9_6.noarch 10/23 Verifying : perl-lib-0.65-481.1.el9_6.ppc64le 11/23 Verifying : cpp-11.5.0-11.el9.ppc64le 12/23 Verifying : gcc-plugin-annobin-11.5.0-11.el9.ppc64le 13/23 Verifying : llvm-libs-20.1.8-3.el9.ppc64le 14/23 Verifying : annobin-12.98-1.el9.ppc64le 15/23 Verifying : gcc-11.5.0-11.el9.ppc64le 16/23 Verifying : libasan-11.5.0-11.el9.ppc64le 17/23 Verifying : libubsan-11.5.0-11.el9.ppc64le 18/23 Verifying : llvm-filesystem-20.1.8-3.el9.ppc64le 19/23 Verifying : ncurses-c++-libs-6.2-12.20210508.el9.ppc64le 20/23 Verifying : ncurses-devel-6.2-12.20210508.el9.ppc64le 21/23 Verifying : glibc-devel-2.34-231.el9_7.2.ppc64le 22/23 Verifying : kernel-headers-5.14.0-611.26.1.el9_7.ppc64le 23/23 Installed products updated. Installed: annobin-12.98-1.el9.ppc64le cpp-11.5.0-11.el9.ppc64le gcc-11.5.0-11.el9.ppc64le gcc-plugin-annobin-11.5.0-11.el9.ppc64le glibc-devel-2.34-231.el9_7.2.ppc64le htslib-1.23-1.el9.ppc64le htslib-devel-1.23-1.el9.ppc64le htslib-tools-1.23-1.el9.ppc64le kernel-headers-5.14.0-611.26.1.el9_7.ppc64le libasan-11.5.0-11.el9.ppc64le libatomic-11.5.0-11.el9.ppc64le libedit-3.1-38.20210216cvs.el9.ppc64le libmpc-1.2.1-4.el9.ppc64le libubsan-11.5.0-11.el9.ppc64le libxcrypt-devel-4.4.18-3.el9.ppc64le llvm-filesystem-20.1.8-3.el9.ppc64le llvm-libs-20.1.8-3.el9.ppc64le make-1:4.3-8.el9.ppc64le ncurses-c++-libs-6.2-12.20210508.el9.ppc64le ncurses-devel-6.2-12.20210508.el9.ppc64le perl-FindBin-1.51-481.1.el9_6.noarch perl-lib-0.65-481.1.el9_6.ppc64le zlib-devel-1.2.11-40.el9.ppc64le Complete! Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1769040000 Wrote: /builddir/build/SRPMS/samtools-1.23-1.el9.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 2.2 kB/s | 1.5 kB 00:00 Red Hat Enterprise Linux - BaseOS 26 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux - AppStream 25 kB/s | 4.5 kB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 32 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 9 - ppc64le 626 kB/s | 23 kB 00:00 Package gcc-11.5.0-11.el9.ppc64le is already installed. Package htslib-devel-1.23-1.el9.ppc64le is already installed. Package htslib-tools-1.23-1.el9.ppc64le is already installed. Package make-1:4.3-8.el9.ppc64le is already installed. Package ncurses-devel-6.2-12.20210508.el9.ppc64le is already installed. Package perl-FindBin-1.51-481.1.el9_6.noarch is already installed. Package perl-Getopt-Long-1:2.52-4.el9.noarch is already installed. Package perl-lib-0.65-481.1.el9_6.ppc64le is already installed. Package perl-interpreter-4:5.32.1-481.1.el9_6.ppc64le is already installed. Package zlib-devel-1.2.11-40.el9.ppc64le is already installed. Dependencies resolved. Nothing to do. Complete! Finish: build setup for samtools-1.23-1.el9.src.rpm Start: rpmbuild samtools-1.23-1.el9.src.rpm Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1769040000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.Sv6Ijo + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf samtools-1.23 + /usr/bin/bzip2 -dc /builddir/build/SOURCES/samtools-1.23.tar.bz2 + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd samtools-1.23 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm -f INSTALL + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.O0HUHi + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.23/configure + diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure + mv ./htslib-1.23/configure.backup ./htslib-1.23/configure + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./htslib-1.23/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./htslib-1.23/config.guess ++ basename ./htslib-1.23/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./htslib-1.23/config.guess '/usr/lib/rpm/redhat/config.guess' -> './htslib-1.23/config.guess' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./htslib-1.23/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./htslib-1.23/config.sub ++ basename ./htslib-1.23/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./htslib-1.23/config.sub '/usr/lib/rpm/redhat/config.sub' -> './htslib-1.23/config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh + ./configure --build=powerpc64le-redhat-linux-gnu --host=powerpc64le-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' --prefix=/usr --with-htslib=system checking for gawk... gawk checking for powerpc64le-redhat-linux-gnu-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc option to enable large file support... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for NcursesW wide-character library... yes checking for working ncursesw/curses.h... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h + /usr/bin/make -O -j5 V=1 VERBOSE=1 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -fasynchronous-unwind-tables -fstack-clash-protection"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 "' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/split/test_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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o bam_checksum.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz -lpthread lto-wrapper: warning: using serial compilation of 10 LTRANS jobs + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.xZFnRP + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le '!=' / ']' + rm -rf /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le ++ dirname /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le + cd samtools-1.23 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/share/man/man1 /usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin /usr/bin/install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin /usr/bin/install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin /usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/share/man/man1 ++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/zoom2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/blast2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/bowtie2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/export2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/fasta-sanitize.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/interpolate_sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/novo2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/plot-ampliconstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/plot-bamstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/psl2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/sam2vcf.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/samtools.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/seq_cache_populate.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/soap2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/wgsim_eval.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/zoom2sam.pl + /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 1.23-1.el9 --unique-debug-suffix -1.23-1.el9.ppc64le --unique-debug-src-base samtools-1.23-1.el9.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.23 extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/maq2sam-long extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/maq2sam-short extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/md5sum-lite extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/md5fa extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/ace2sam extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/samtools extracting debug info from /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/bin/wgsim original debug info size: 2688kB, size after compression: 2496kB /usr/bin/sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match. 3173 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.Oy2VLv + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + ldd samtools + grep -E -e '/lib(64)?/libhts\.so\.' -e '/lib64/lp64d/libhts\.so\.' libhts.so.3 => /lib64/libhts.so.3 (0x00007fffaef20000) + make test test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip= ${TEST_OPTS:-} test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /builddir/build/BUILD/samtools-1.23/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok bgzip -c -b 65272 -s 5 /tmp/IqVumMuIjE/bgzip.dat.gz .. ok bgzip -c -b 979200 -s 6 /tmp/IqVumMuIjE/bgzip.dat.gz .. ok bgzip -c -b 652804 -s 6 /tmp/IqVumMuIjE/bgzip.dat.gz .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/IqVumMuIjE/faidx.fa 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/IqVumMuIjE/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/IqVumMuIjE/faidx.fa 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/IqVumMuIjE/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/IqVumMuIjE/faidx.fa 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/IqVumMuIjE/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/IqVumMuIjE/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools faidx /tmp/IqVumMuIjE/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/IqVumMuIjE/fqidx.fq 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/IqVumMuIjE/fqidx.fq.gz 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/IqVumMuIjE/fqidx.fq 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/IqVumMuIjE/fqidx.fq.gz 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/IqVumMuIjE/fqidx.fq 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/IqVumMuIjE/fqidx.fq.gz 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/IqVumMuIjE/fqidx.fq 1:99998-100007 .. ok .. ok /builddir/build/BUILD/samtools-1.23/samtools fqidx /tmp/IqVumMuIjE/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /builddir/build/BUILD/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /builddir/build/BUILD/samtools-1.23/test/dat/dict.fa .. ok test_dict: /builddir/build/BUILD/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/IqVumMuIjE/dict.fa.gz .. ok test_dict: cat /builddir/build/BUILD/samtools-1.23/test/dat/dict.fa | /builddir/build/BUILD/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /builddir/build/BUILD/samtools-1.23/samtools dict -AH < /builddir/build/BUILD/samtools-1.23/test/dat/dict.alias.fa .. ok test_dict: /builddir/build/BUILD/samtools-1.23/samtools dict -H -l /builddir/build/BUILD/samtools-1.23/test/dat/dict.alt < /builddir/build/BUILD/samtools-1.23/test/dat/dict.alias.fa .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view /tmp/IqVumMuIjE/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view /tmp/IqVumMuIjE/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/IqVumMuIjE/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/IqVumMuIjE/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools merge -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai /tmp/IqVumMuIjE/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/IqVumMuIjE/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam && cat /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -c /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam /tmp/IqVumMuIjE/auto_indexed.csi && cat /tmp/IqVumMuIjE/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.cram /tmp/IqVumMuIjE/auto_indexed.crai && cat /tmp/IqVumMuIjE/auto_indexed.crai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -c /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.sam /tmp/IqVumMuIjE/auto_indexed.csi && cat /tmp/IqVumMuIjE/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 /tmp/IqVumMuIjE/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 /tmp/IqVumMuIjE/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/IqVumMuIjE/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/IqVumMuIjE/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai /tmp/IqVumMuIjE/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /tmp/IqVumMuIjE/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -@ 2 -M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam && cat /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam /tmp/IqVumMuIjE/auto_indexed.csi && cat /tmp/IqVumMuIjE/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.cram /tmp/IqVumMuIjE/auto_indexed.crai && cat /tmp/IqVumMuIjE/auto_indexed.crai .. ok test_index: /builddir/build/BUILD/samtools-1.23/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.sam /tmp/IqVumMuIjE/auto_indexed.csi && cat /tmp/IqVumMuIjE/auto_indexed.csi .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/IqVumMuIjE/mpileup.bam.list -f /tmp/IqVumMuIjE/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/IqVumMuIjE/mpileup.cram.list -f /tmp/IqVumMuIjE/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/IqVumMuIjE/mpileup.bam.urllist -f /tmp/IqVumMuIjE/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -b /tmp/IqVumMuIjE/mpileup.cram.urllist -f /tmp/IqVumMuIjE/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/IqVumMuIjE/mpileup.ref.fa.gz -r17:1050-1060 /tmp/IqVumMuIjE/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/IqVumMuIjE/mpileup.ref.fa.gz -r17:1050-1060 /tmp/IqVumMuIjE/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.23/samtools mpileup /builddir/build/BUILD/samtools-1.23/test/mpileup/overlap.bam | grep 128814202 test/test.pl: no IO::Pty module or can't open pty; skipping usage tests .. ok test_usage: samtools test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/IqVumMuIjE/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/IqVumMuIjE/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/IqVumMuIjE/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/IqVumMuIjE/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/IqVumMuIjE/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/IqVumMuIjE/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/IqVumMuIjE/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/IqVumMuIjE/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/IqVumMuIjE/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/IqVumMuIjE/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/IqVumMuIjE/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/IqVumMuIjE/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/IqVumMuIjE/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/IqVumMuIjE/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/IqVumMuIjE/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/IqVumMuIjE/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/IqVumMuIjE/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/IqVumMuIjE/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/IqVumMuIjE/view.001.forn (SAM input) .. ok 68: Count -N /tmp/IqVumMuIjE/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/IqVumMuIjE/view.001.forn (BAM input) .. ok 70: Count -N /tmp/IqVumMuIjE/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/IqVumMuIjE/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/IqVumMuIjE/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/IqVumMuIjE/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/IqVumMuIjE/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/IqVumMuIjE/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/IqVumMuIjE/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/IqVumMuIjE/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/IqVumMuIjE/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/IqVumMuIjE/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/IqVumMuIjE/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/IqVumMuIjE/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/IqVumMuIjE/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/IqVumMuIjE/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/IqVumMuIjE/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/IqVumMuIjE/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/IqVumMuIjE/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/IqVumMuIjE/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/IqVumMuIjE/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/IqVumMuIjE/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/IqVumMuIjE/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/IqVumMuIjE/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/IqVumMuIjE/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/IqVumMuIjE/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/IqVumMuIjE/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/IqVumMuIjE/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/IqVumMuIjE/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok 110: Count -d NE:TGCA (SAM input) .. ok 111: Filter -d NE:TGCA (BAM input) .. ok 112: Count -d NE:TGCA (BAM input) .. ok 113: Filter -d NE:TGCA (CRAM input) .. ok 114: Count -d NE:TGCA (CRAM input) .. ok 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/IqVumMuIjE/view.test115.sam -h -d TGCA /tmp/IqVumMuIjE/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -d TGCA /tmp/IqVumMuIjE/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/IqVumMuIjE/view.test117.sam -h -d TGCA /tmp/IqVumMuIjE/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -d TGCA /tmp/IqVumMuIjE/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/IqVumMuIjE/view.test119.sam -h -d TGCA /tmp/IqVumMuIjE/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -d TGCA /tmp/IqVumMuIjE/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/IqVumMuIjE/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/IqVumMuIjE/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/IqVumMuIjE/view.test121.sam -h -D BClong:/tmp/IqVumMuIjE/view.001.fobc /tmp/IqVumMuIjE/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/IqVumMuIjE/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/IqVumMuIjE/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/IqVumMuIjE/view.001.fobc /tmp/IqVumMuIjE/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/IqVumMuIjE/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/IqVumMuIjE/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/IqVumMuIjE/view.test123.sam -h -D BClong:/tmp/IqVumMuIjE/view.001.fobc /tmp/IqVumMuIjE/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/IqVumMuIjE/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/IqVumMuIjE/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/IqVumMuIjE/view.001.fobc /tmp/IqVumMuIjE/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/IqVumMuIjE/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/IqVumMuIjE/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/IqVumMuIjE/view.test125.sam -h -D BClong:/tmp/IqVumMuIjE/view.001.fobc /tmp/IqVumMuIjE/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/IqVumMuIjE/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/IqVumMuIjE/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -D BClong:/tmp/IqVumMuIjE/view.001.fobc /tmp/IqVumMuIjE/view.test006.cram --no-PG .. expected failure 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/IqVumMuIjE/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/IqVumMuIjE/view.001.sam --no-PG .. expected failure 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/IqVumMuIjE/view.001.sam --no-PG .. expected failure 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/IqVumMuIjE/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/IqVumMuIjE/view.test001.bam --no-PG .. expected failure 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/IqVumMuIjE/view.test001.bam --no-PG .. expected failure 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -o /tmp/IqVumMuIjE/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/IqVumMuIjE/view.test006.cram --no-PG .. expected failure 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/IqVumMuIjE/view.test006.cram --no-PG .. expected failure 133: Filter -d NM:13 (SAM input) .. ok 134: Count -d NM:13 (SAM input) .. ok 135: Filter -d NM:13 (BAM input) .. ok 136: Count -d NM:13 (BAM input) .. ok 137: Filter -d NM:13 (CRAM input) .. ok 138: Count -d NM:13 (CRAM input) .. ok 139: Filter -d ab:z (SAM input) .. ok 140: Count -d ab:z (SAM input) .. ok 141: Filter -d ab:z (BAM input) .. ok 142: Count -d ab:z (BAM input) .. ok 143: Filter -d ab:z (CRAM input) .. ok 144: Count -d ab:z (CRAM input) .. ok 145: Filter -l Library 2 (SAM input) .. ok 146: Count -l Library 2 (SAM input) .. ok 147: Filter -l Library 2 (BAM input) .. ok 148: Count -l Library 2 (BAM input) .. ok 149: Filter -l Library 2 (CRAM input) .. ok 150: Count -l Library 2 (CRAM input) .. ok 151: Filter -l Library 3 (SAM input) .. ok 152: Count -l Library 3 (SAM input) .. ok 153: Filter -l Library 3 (BAM input) .. ok 154: Count -l Library 3 (BAM input) .. ok 155: Filter -l Library 3 (CRAM input) .. ok 156: Count -l Library 3 (CRAM input) .. ok 157: Filter -q 50 (SAM input) .. ok 158: Count -q 50 (SAM input) .. ok 159: Filter -q 50 (BAM input) .. ok 160: Count -q 50 (BAM input) .. ok 161: Filter -q 50 (CRAM input) .. ok 162: Count -q 50 (CRAM input) .. ok 163: Filter -q 99 (SAM input) .. ok 164: Count -q 99 (SAM input) .. ok 165: Filter -q 99 (BAM input) .. ok 166: Count -q 99 (BAM input) .. ok 167: Filter -q 99 (CRAM input) .. ok 168: Count -q 99 (CRAM input) .. ok 169: Filter -q 100 (SAM input) .. ok 170: Count -q 100 (SAM input) .. ok 171: Filter -q 100 (BAM input) .. ok 172: Count -q 100 (BAM input) .. ok 173: Filter -q 100 (CRAM input) .. ok 174: Count -q 100 (CRAM input) .. ok 175: Filter -x fa (SAM input) .. ok 176: Count -x fa (SAM input) .. ok 177: Filter -x fa (BAM input) .. ok 178: Count -x fa (BAM input) .. ok 179: Filter -x fa (CRAM input) .. ok 180: Count -x fa (CRAM input) .. ok 181: Filter -x fa -x ha (SAM input) .. ok 182: Count -x fa -x ha (SAM input) .. ok 183: Filter -x fa -x ha (BAM input) .. ok 184: Count -x fa -x ha (BAM input) .. ok 185: Filter -x fa -x ha (CRAM input) .. ok 186: Count -x fa -x ha (CRAM input) .. ok 187: Filter -x fa,ha (SAM input) .. ok 188: Count -x fa,ha (SAM input) .. ok 189: Filter -x fa,ha (BAM input) .. ok 190: Count -x fa,ha (BAM input) .. ok 191: Filter -x fa,ha (CRAM input) .. ok 192: Count -x fa,ha (CRAM input) .. ok 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 205: Filter -x fa -r grp2 (SAM input) .. ok 206: Count -x fa -r grp2 (SAM input) .. ok 207: Filter -x fa -r grp2 (BAM input) .. ok 208: Count -x fa -r grp2 (BAM input) .. ok 209: Filter -x fa -r grp2 (CRAM input) .. ok 210: Count -x fa -r grp2 (CRAM input) .. ok 211: Filter -x RG -r grp2 (SAM input) .. ok 212: Count -x RG -r grp2 (SAM input) .. ok 213: Filter -x RG -r grp2 (BAM input) .. ok 214: Count -x RG -r grp2 (BAM input) .. ok 215: Filter -x RG -r grp2 (CRAM input) .. ok 216: Count -x RG -r grp2 (CRAM input) .. ok 217: Filter -m 10 (SAM input) .. ok 218: Count -m 10 (SAM input) .. ok 219: Filter -m 10 (BAM input) .. ok 220: Count -m 10 (BAM input) .. ok 221: Filter -m 10 (CRAM input) .. ok 222: Count -m 10 (CRAM input) .. ok 223: Filter -m 11 (SAM input) .. ok 224: Count -m 11 (SAM input) .. ok 225: Filter -m 11 (BAM input) .. ok 226: Count -m 11 (BAM input) .. ok 227: Filter -m 11 (CRAM input) .. ok 228: Count -m 11 (CRAM input) .. ok 229: Filter -m 15 (SAM input) .. ok 230: Count -m 15 (SAM input) .. ok 231: Filter -m 15 (BAM input) .. ok 232: Count -m 15 (BAM input) .. ok 233: Filter -m 15 (CRAM input) .. ok 234: Count -m 15 (CRAM input) .. ok 235: Filter -m 16 (SAM input) .. ok 236: Count -m 16 (SAM input) .. ok 237: Filter -m 16 (BAM input) .. ok 238: Count -m 16 (BAM input) .. ok 239: Filter -m 16 (CRAM input) .. ok 240: Count -m 16 (CRAM input) .. ok 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 247: Filter -e [BC] (SAM input) .. ok 248: Count -e [BC] (SAM input) .. ok 249: Filter -e [BC] (BAM input) .. ok 250: Count -e [BC] (BAM input) .. ok 251: Filter -e [BC] (CRAM input) .. ok 252: Count -e [BC] (CRAM input) .. ok 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 259: Filter -e mapq >= 50 (SAM input) .. ok 260: Count -e mapq >= 50 (SAM input) .. ok 261: Filter -e mapq >= 50 (BAM input) .. ok 262: Count -e mapq >= 50 (BAM input) .. ok 263: Filter -e mapq >= 50 (CRAM input) .. ok 264: Count -e mapq >= 50 (CRAM input) .. ok 265: Filter -e mapq >= 99 (SAM input) .. ok 266: Count -e mapq >= 99 (SAM input) .. ok 267: Filter -e mapq >= 99 (BAM input) .. ok 268: Count -e mapq >= 99 (BAM input) .. ok 269: Filter -e mapq >= 99 (CRAM input) .. ok 270: Count -e mapq >= 99 (CRAM input) .. ok 271: Filter -e mapq >= 100 (SAM input) .. ok 272: Count -e mapq >= 100 (SAM input) .. ok 273: Filter -e mapq >= 100 (BAM input) .. ok 274: Count -e mapq >= 100 (BAM input) .. ok 275: Filter -e mapq >= 100 (CRAM input) .. ok 276: Count -e mapq >= 100 (CRAM input) .. ok 277: 1bp reads file SAM -> BAM -> SAM .. ok 278: 1bp reads file SAM -> CRAM -> SAM .. ok 278: Region Z (BAM input) .. ok 279: Count Z (BAM input) .. ok 280: Region Z (CRAM input) .. ok 281: Count Z (CRAM input) .. ok 282: Region Z:30 (BAM input) .. ok 283: Count Z:30 (BAM input) .. ok 284: Region Z:30 (CRAM input) .. ok 285: Count Z:30 (CRAM input) .. ok 286: Region Z:20-40 (BAM input) .. ok 287: Count Z:20-40 (BAM input) .. ok 288: Region Z:20-40 (CRAM input) .. ok 289: Count Z:20-40 (CRAM input) .. ok 290: Region ref1 (BAM input) .. ok 291: Count ref1 (BAM input) .. ok 292: Region ref1 (CRAM input) .. ok 293: Count ref1 (CRAM input) .. ok 294: Region ref1:15 (BAM input) .. ok 295: Count ref1:15 (BAM input) .. ok 296: Region ref1:15 (CRAM input) .. ok 297: Count ref1:15 (CRAM input) .. ok 298: Region ref1:15-45 (BAM input) .. ok 299: Count ref1:15-45 (BAM input) .. ok 300: Region ref1:15-45 (CRAM input) .. ok 301: Count ref1:15-45 (CRAM input) .. ok 302: Region ref1:15-45 ref2 (BAM input) .. ok 303: Count ref1:15-45 ref2 (BAM input) .. ok 304: Region ref1:15-45 ref2 (CRAM input) .. ok 305: Count ref1:15-45 ref2 (CRAM input) .. ok 306: Region ref1:15-45 ref2:16 (BAM input) .. ok 307: Count ref1:15-45 ref2:16 (BAM input) .. ok 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 318: Region -f 128 ref1 (BAM input) .. ok 319: Count -f 128 ref1 (BAM input) .. ok 320: Region -f 128 ref1 (CRAM input) .. ok 321: Count -f 128 ref1 (CRAM input) .. ok 322: Region -q 50 ref1:15-45 (BAM input) .. ok 323: Count -q 50 ref1:15-45 (BAM input) .. ok 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 326: Region -r grp2 ref1:15-45 (BAM input) .. ok 327: Count -r grp2 ref1:15-45 (BAM input) .. ok 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok 330: Region * (BAM input) .. ok 331: Count * (BAM input) .. ok 332: Region * (CRAM input) .. ok 333: Count * (CRAM input) .. ok 334: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.03.bed (BAM input).. ok 351: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.03.bed (BAM input).. ok 352: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.03.bed (CRAM input).. ok 353: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.03.bed (CRAM input).. ok 354: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z (BAM input).. ok 355: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z (BAM input).. ok 356: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z (CRAM input).. ok 357: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z (CRAM input).. ok 358: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:30 (BAM input).. ok 359: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:30 (BAM input).. ok 360: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 361: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 362: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 363: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 364: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 365: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 366: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 367: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 368: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 369: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 370: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 371: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 372: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 373: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 374: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref2 (BAM input).. ok 375: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref2 (BAM input).. ok 376: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref2 (CRAM input).. ok 377: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref2 (CRAM input).. ok 378: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 379: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 380: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 381: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 382: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 383: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 384: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 385: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 386: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -f 128 (BAM input).. ok 387: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -f 128 (BAM input).. ok 388: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 389: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 390: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -q 5 (BAM input).. ok 391: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -q 5 (BAM input).. ok 392: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 393: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 394: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 395: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 396: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 397: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 398: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 399: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 400: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 401: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 402: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 403: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 404: Region -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 405: Count -L /builddir/build/BUILD/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 406: -L with nested regions .. ok 407: Make BAM with no M5/UR tags .. ok 408: Add @SQ with -t (SAM -> SAM) .. ok 409: Add @SQ with -T (SAM -> SAM) .. ok 410: Add @SQ with -t (BAM -> SAM) .. ok 411: Add @SQ with -T (BAM -> SAM) .. ok 412: Add @SQ with -t (SAM -> BAM) .. ok 413: Add @SQ with -T (SAM -> BAM) .. ok 414: Add @SQ with -t (BAM -> BAM) .. ok 415: Add @SQ with -T (BAM -> BAM) .. ok 416: Add @SQ with -t (SAM -> CRAM) .. ok 417: Add @SQ with -T (SAM -> CRAM) .. ok 418: Add @SQ with -t (BAM -> CRAM) .. ok 419: Add @SQ with -T (BAM -> CRAM) .. ok 420: Make CRAM with no UR field .. ok 421: Decoding CRAM with no UR field via -T .. ok 422: CIGAR B-operator removal .. ok 423: Big SAM -> BAM .. ok 424: Big SAM -> BAM (2 threads) .. ok 425: Big SAM -> BAM (4 threads) .. ok 426: Big SAM -> CRAM .. ok 427: Big SAM -> CRAM (2 threads) .. ok 428: Big SAM -> CRAM (4 threads) .. ok 429: Subsample 0.2 (SAM input) ............ ok 430: Subsample 0.5 (SAM input) ............ ok 431: Subsample 0.8 (SAM input) ............ ok 432: Subsample 0.2 (BAM input) ............ ok 433: Subsample 0.5 (BAM input) ............ ok 434: Subsample 0.8 (BAM input) ............ ok 435: Subsample 0.2 (CRAM input) ............ ok 436: Subsample 0.5 (CRAM input) ............ ok 437: Subsample 0.8 (CRAM input) ............ ok 438: SAM add PG .. ok 439: Unset dup flag, remove dt and do tags .. ok 440: Unmap dup flagged reads. .. ok 441: Unmap dup flagged reads. .. ok 442: fetch pairs .. ok 443: fetch pairs .. ok 444: fetch pairs .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -h 0 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -h 1 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -h 5 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -h 29 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -h 30 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -n 0 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -n 1 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -n 5 /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.23/samtools head -h 5 -n 5 < /builddir/build/BUILD/samtools-1.23/test/dat/view.001.sam .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate BAM region file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate BAM region file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate BAM region file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate BAM region file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat CRAM subregion files .. ok 5: cat BAM files to stdout .. ok 6: cat recompressed BAM files to stdout .. ok 7: cat CRAM files to stdout .. ok 8: cat CRAM subregion files to stdout .. ok 9: cat CRAM part 1/2 .. ok 9: cat CRAM part 2/2 .. ok 9: cat CRAM parts 1/2 + 2/2 .. ok 10: cat BAM files with new header .. ok 11: cat recompressed BAM files with new header .. ok 12: cat CRAM files with new header .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -0 /builddir/build/BUILD/samtools-1.23/test/0.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -0 /builddir/build/BUILD/samtools-1.23/test/0.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -s /builddir/build/BUILD/samtools-1.23/test/s.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T RG,BC,QT -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T RG,BC,QT,MD,ia -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/2.interleaved.fq -T "" .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/3.interleaved.fq -i .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/4.aux.fq -T "*" .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/4.aux.fq -T "" .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -U test/bam2fq/UMI.fq.expected .. ok test_import: /builddir/build/BUILD/samtools-1.23/samtools import --no-PG -U --UMI-tag OX test/bam2fq/UMI.fq.expected .. ok test_bam2fq: Generate BAM file .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.23/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -t -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.703.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.23/test/o.fq -2 /builddir/build/BUILD/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fasta -N -1 /builddir/build/BUILD/samtools-1.23/test/o.fa -2 /builddir/build/BUILD/samtools-1.23/test/o.fa /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -o /builddir/build/BUILD/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -s /tmp/IqVumMuIjE/bam2fq.discard.s.fq -0 /tmp/IqVumMuIjE/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.013.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.23/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.23/test/i2.fq -0 /builddir/build/BUILD/samtools-1.23/test/0.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.014.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T '' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -t -T '*' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T '*' -d MD:10 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T '*' -d NM:0 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -N -T '*' -d ia /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -d NM:13 -d NM:14 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -D NM:test/dat/bam2fq.NM-D /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -D MD:test/dat/bam2fq.MD-D /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -O --no-sc --no-sc-bkp -T 's0' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -O --no-sc -T's0' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -O --no-sc /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -O --no-sc --sc-aux s1 -T's0,s1' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -U test/import/UMI.expected.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -U --UMI-tag RX,OX test/import/UMI-OX.expected.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.23/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -t -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.703.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -1 /builddir/build/BUILD/samtools-1.23/test/o.fq -2 /builddir/build/BUILD/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fasta -@ 2 -N -1 /builddir/build/BUILD/samtools-1.23/test/o.fa -2 /builddir/build/BUILD/samtools-1.23/test/o.fa /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -o /builddir/build/BUILD/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -s /tmp/IqVumMuIjE/bam2fq.discard.s.fq -0 /tmp/IqVumMuIjE/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.013.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.23/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.23/test/i2.fq -0 /builddir/build/BUILD/samtools-1.23/test/0.fq /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.014.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -T '' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -t -T '*' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -T '*' -d MD:10 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -T '*' -d NM:0 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -N -T '*' -d ia /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -d NM:13 -d NM:14 /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -O --no-sc --no-sc-bkp -T 's0' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -O --no-sc -T's0' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -O --no-sc /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -@ 2 -O --no-sc --sc-aux s1 -T's0,s1' /builddir/build/BUILD/samtools-1.23/test/dat/bam2fq.sc.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -U test/import/UMI.expected.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.23/samtools fastq -U --UMI-tag RX,OX test/import/UMI-OX.expected.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa -i 0 /builddir/build/BUILD/samtools-1.23/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -t /builddir/build/BUILD/samtools-1.23/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -g 4 -t /builddir/build/BUILD/samtools-1.23/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -g 4 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.23/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.23/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.23/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.23/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /builddir/build/BUILD/samtools-1.23/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /builddir/build/BUILD/samtools-1.23/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /builddir/build/BUILD/samtools-1.23/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -I s1 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -I grp2 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -I grp3 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -I Sample /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23/test/mpileup/ce.fa /builddir/build/BUILD/samtools-1.23/test/stat/15.big_del.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam | grep -e"^RFS" .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23/test/stat/test.fa ERR: [E::faidx_adjust_position] The sequence "ref1" was not found Failed to fetch the sequence "ref1" .. expected failure test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa | grep -e"^RFS" .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats --ref-stats-chunk -1 /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa | grep -e"^RFS" .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa alpha:10-20 | grep -e"^RFS" .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa -t /builddir/build/BUILD/samtools-1.23/test/stat/11.stats.targets | grep -e"^RFS" .. ok test_stats: /builddir/build/BUILD/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23/test/stat/11_target.bam -r /builddir/build/BUILD/samtools-1.23/test/stat/test1.fa -t /builddir/build/BUILD/samtools-1.23/test/stat/11.stats.targets ref1 | grep -e"^RFS" .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam -b /tmp/unIFUPVjtl - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/IqVumMuIjE/merge.tag.1.bam /tmp/IqVumMuIjE/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/IqVumMuIjE/merge.tag.3.bam /tmp/IqVumMuIjE/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge --no-PG -O SAM - /builddir/build/BUILD/samtools-1.23/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.23/test/merge/merge.bed - /tmp/IqVumMuIjE/merge.bed.1.bam /tmp/IqVumMuIjE/merge.bed.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge --no-PG -r -O SAM - /builddir/build/BUILD/samtools-1.23/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge --no-PG -O SAM --template-coordinate - /builddir/build/BUILD/samtools-1.23/test/merge/test_template_coordinate.1.sam /builddir/build/BUILD/samtools-1.23/test/merge/test_template_coordinate.2.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam -b /tmp/zI4os9FN2o - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/IqVumMuIjE/merge.tag.1.bam /tmp/IqVumMuIjE/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/IqVumMuIjE/merge.tag.3.bam /tmp/IqVumMuIjE/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM - /builddir/build/BUILD/samtools-1.23/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.23/test/merge/merge.bed - /tmp/IqVumMuIjE/merge.bed.1.bam /tmp/IqVumMuIjE/merge.bed.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 --no-PG -r -O SAM - /builddir/build/BUILD/samtools-1.23/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /builddir/build/BUILD/samtools-1.23/test/merge/test_template_coordinate.1.sam /builddir/build/BUILD/samtools-1.23/test/merge/test_template_coordinate.2.sam .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/IqVumMuIjE/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -f /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/IqVumMuIjE/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -o /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/IqVumMuIjE/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -N -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -t RG -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -n -t RG -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -t AS -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -t FI -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort --template-coordinate -m 10M /builddir/build/BUILD/samtools-1.23/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -m 10M -M -K10 -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -m 10M -M -K10 -I /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -m 10M -MH -K10 -I /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/IqVumMuIjE/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/IqVumMuIjE/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam /tmp/IqVumMuIjE/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -N -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -t RG -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -n -t RG -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -t AS -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -t FI -m 10M /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 --template-coordinate -m 10M /builddir/build/BUILD/samtools-1.23/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -m 10M -M -K10 -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -m 10M -M -K10 -I /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -m 10M -MH -K10 -I /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate --output-fmt=sam -O /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -o /builddir/build/BUILD/samtools-1.23/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -o /builddir/build/BUILD/samtools-1.23/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate --output-fmt=sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate --output-fmt=sam -f /builddir/build/BUILD/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 --output-fmt=sam -O /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.23/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.23/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 --output-fmt=sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 --output-fmt=sam -f /builddir/build/BUILD/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.23/samtools collate -@ 2 --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.23/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.23/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/sanitize.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_draft.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_bounds.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.23/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.23/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/sanitize.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_draft.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23/test/fixmate/mod_bounds.sam - .. ok /builddir/build/BUILD/samtools-1.23/samtools calmd -uAr /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa .. ok /builddir/build/BUILD/samtools-1.23/samtools calmd -@ 2 -uAr /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.ref.fa .. ok test_idxstat: /builddir/build/BUILD/samtools-1.23/samtools idxstats /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam .. ok test_idxstat: /builddir/build/BUILD/samtools-1.23/samtools idxstats /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.cram .. ok test_idxstat: /builddir/build/BUILD/samtools-1.23/samtools idxstats /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.sam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck -v /builddir/build/BUILD/samtools-1.23/test/quickcheck/1.quickcheck.badeof.bam /builddir/build/BUILD/samtools-1.23/test/quickcheck/2.quickcheck.badheader.bam /builddir/build/BUILD/samtools-1.23/test/quickcheck/3.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.23/test/quickcheck/4.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.23/test/quickcheck/5.quickcheck.scramble30.truncated.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/6.quickcheck.cram21.ok.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/7.quickcheck.cram30.ok.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/8.quickcheck.cram21.truncated.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/9.quickcheck.cram30.truncated.cram /builddir/build/BUILD/samtools-1.23/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.23/samtools quickcheck -uv /builddir/build/BUILD/samtools-1.23/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v21.cram | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader --in-place /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v21.cram && /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader --in-place /builddir/build/BUILD/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v30.cram && /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.23/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.23/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -m orphan_only /builddir/build/BUILD/samtools-1.23/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -R '1#9' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.23/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.23/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -m orphan_only /builddir/build/BUILD/samtools-1.23/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -R '1#9' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.23/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.23/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.23/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.23/test/addrprg/1_fixup.sam .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/3_missing_mc.sam - ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. samtools markdup: error, unable to assign pair hash key. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/4_missing_ms.sam - ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -O sam -r --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/8_optical_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.23/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.23/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/17_read_group.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /builddir/build/BUILD/samtools-1.23/test/markdup/18_primary_duplicate_count.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/3_missing_mc.sam - ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. samtools markdup: error, unable to assign pair hash key. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/4_missing_ms.sam - ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -O sam -r --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/8_optical_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.23/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.23/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /builddir/build/BUILD/samtools-1.23/test/markdup/17_read_group.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.23/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /builddir/build/BUILD/samtools-1.23/test/markdup/18_primary_duplicate_count.sam - .. ok test_bedcov: /builddir/build/BUILD/samtools-1.23/samtools bedcov /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.23/samtools bedcov -j /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.23/samtools bedcov -g512 -G2048 /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.23/samtools bedcov -c /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.23/test/bedcov/bedcov.bam .. ok .. ok .. ok .. ok .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -p 5 -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -d RG -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -d an -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -d an -M 3 -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.unk.sam /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools sort -t nn /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam | /builddir/build/BUILD/samtools-1.23/samtools split --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam - .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -p 5 -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -d RG -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -d an -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.unk.sam /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam .. ok test_split: /builddir/build/BUILD/samtools-1.23/samtools sort -@ 2 -t nn /builddir/build/BUILD/samtools-1.23/test/split/split_d_nn.sam | /builddir/build/BUILD/samtools-1.23/samtools split -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam - .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /tmp/IqVumMuIjE/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG /tmp/IqVumMuIjE/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools view -h --no-PG -L /builddir/build/BUILD/samtools-1.23/test/large_pos/test.bed /tmp/IqVumMuIjE/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools sort -O sam --no-PG -m 10M /builddir/build/BUILD/samtools-1.23/test/large_pos/longref_name.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools merge -O sam --no-PG - /builddir/build/BUILD/samtools-1.23/test/large_pos/longref.sam /builddir/build/BUILD/samtools-1.23/test/large_pos/longref2.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools depth /builddir/build/BUILD/samtools-1.23/test/large_pos/longref.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools depth -b /builddir/build/BUILD/samtools-1.23/test/large_pos/test.bed /builddir/build/BUILD/samtools-1.23/test/large_pos/longref.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/IqVumMuIjE/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.23/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /builddir/build/BUILD/samtools-1.23/samtools fixmate -O sam --no-PG - - | /builddir/build/BUILD/samtools-1.23/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test2.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test2.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.23/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_hard_clipped.expected.sam /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_soft_clipped.expected.sam /builddir/build/BUILD/samtools-1.23/test/ampliconclip/1_soft_clipped_strand.expected.sam /builddir/build/BUILD/samtools-1.23/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.23/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.23/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag | /builddir/build/BUILD/samtools-1.23/samtools view .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag < /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23/samtools view .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23/samtools view .. ok test_reset: cat /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.bam .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam /builddir/build/BUILD/samtools-1.23/test/dat/test_input_1_a.cram .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG sam_to_fixed_bam /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index --no-PG /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23/test/reset/output.tmp.sam -e"@PG" .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset --dupflag /builddir/build/BUILD/samtools-1.23/test/reset/seq.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_reset: /builddir/build/BUILD/samtools-1.23/samtools reset /builddir/build/BUILD/samtools-1.23/test/reset/seq.sam -o /builddir/build/BUILD/samtools-1.23/test/reset/output .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum /builddir/build/BUILD/samtools-1.23/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -a /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -qv /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -qv -a /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -m /builddir/build/BUILD/samtools-1.23/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -m /builddir/build/BUILD/samtools-1.23/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 /builddir/build/BUILD/samtools-1.23/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -a /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -qv /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -qv -a /builddir/build/BUILD/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -m /builddir/build/BUILD/samtools-1.23/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /builddir/build/BUILD/samtools-1.23/samtools checksum -@ 2 -m /builddir/build/BUILD/samtools-1.23/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_coverage: /builddir/build/BUILD/samtools-1.23/samtools coverage /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam .. ok test_coverage: /builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 1 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam .. ok test_coverage: /builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 2 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam .. ok test_coverage: /builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 2 -Q 8 -q 45 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam .. ok test_coverage: /builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 1 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam /tmp/IqVumMuIjE/sample1.sam .. ok test_coverage: /builddir/build/BUILD/samtools-1.23/samtools coverage --min-depth 4 /builddir/build/BUILD/samtools-1.23/test/dat/sample.sam /tmp/IqVumMuIjE/sample1.sam .. ok Number of tests: total .. 998 passed .. 966 failed .. 0 expected failure .. 32 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="gawk" ../regression.sh mpileup.reg === Testing mpileup.reg regressions === [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 120 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="gawk" ../regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 55 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="gawk" ../regression.sh cram-size.reg === Testing cram-size.reg regressions === Expected passes: 5 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/consensus && AWK="gawk" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 77 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/consensus && AWK="gawk" PARAM="-@4 -Z4" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 77 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/cram_size && AWK="gawk" ../regression.sh cram_size.reg === Testing cram_size.reg regressions === Expected passes: 3 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS + RPM_EC=0 ++ jobs -p + exit 0 Processing files: samtools-1.23-1.el9.ppc64le Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.W2u9rP + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + DOCDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/share/doc/samtools + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/share/doc/samtools + cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/share/doc/samtools + cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/share/doc/samtools + cp -pr NEWS.md /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/share/doc/samtools + cp -pr examples/ /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/share/doc/samtools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.5vYyxm + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/share/licenses/samtools + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/share/licenses/samtools + cp -pr LICENSE /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le/usr/share/licenses/samtools + RPM_EC=0 ++ jobs -p + exit 0 Provides: samtools = 1.23-1.el9 samtools(ppc-64) = 1.23-1.el9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(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.el9.ppc64le Provides: samtools-debugsource = 1.23-1.el9 samtools-debugsource(ppc-64) = 1.23-1.el9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: samtools-debuginfo-1.23-1.el9.ppc64le Provides: debuginfo(build-id) = 1dd191392e4487f38916b1139a74af60d1815b6e debuginfo(build-id) = 3bf5d079529955c92fdd4b9ecbb69ae90081d8b4 debuginfo(build-id) = 3f4d5ff8942aa7a944d0f440370de9bc6a676809 debuginfo(build-id) = 75c0047c80c09ac76499e850c8c6f476b76615e5 debuginfo(build-id) = b76e725f6cecf883bc3dc5f731ff0ff277834d0e debuginfo(build-id) = d68bc16ed0d88f300a1c14d76265d8542212f116 debuginfo(build-id) = e344035db297705c01317089fe8a11f845b3f87a samtools-debuginfo = 1.23-1.el9 samtools-debuginfo(ppc-64) = 1.23-1.el9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: samtools-debugsource(ppc-64) = 1.23-1.el9 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le Wrote: /builddir/build/RPMS/samtools-1.23-1.el9.ppc64le.rpm Wrote: /builddir/build/RPMS/samtools-debuginfo-1.23-1.el9.ppc64le.rpm Wrote: /builddir/build/RPMS/samtools-debugsource-1.23-1.el9.ppc64le.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.uFEdXJ + umask 022 + cd /builddir/build/BUILD + cd samtools-1.23 + /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.23-1.el9.ppc64le + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild samtools-1.23-1.el9.src.rpm Finish: build phase for samtools-1.23-1.el9.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-9-ppc64le-1769509438.093451/root/var/log/dnf.rpm.log /var/lib/mock/rhel+epel-9-ppc64le-1769509438.093451/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-9-ppc64le-1769509438.093451/root/var/log/dnf.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/samtools-1.23-1.el9.src.rpm) Config(child) 2 minutes 16 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "samtools-debuginfo", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "ppc64le" }, { "name": "samtools", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "ppc64le" }, { "name": "samtools-debugsource", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "ppc64le" }, { "name": "samtools", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "src" } ] } RPMResults finished