Warning: Permanently added '2620:52:6:1161:dead:beef:cafe:c154' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/10066099-epel-9-ppc64le --chroot epel-9-ppc64le Version: 1.6 PID: 4006 Logging PID: 4008 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 10066099, 'buildroot_pkgs': [], 'chroot': 'epel-9-ppc64le', 'enable_net': False, 'fedora_review': False, 'git_hash': '7f908d99caaa698e4edc070e538303e597a5ee85', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/htslib', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'htslib', 'package_version': '1.23-1', 'project_dirname': 'bioinformatics', 'project_name': 'bioinformatics', 'project_owner': 'ron', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ron/bioinformatics/epel-9-ppc64le/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'ron/bioinformatics--ron', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'ron', 'tags': ['arch_power9'], 'task_id': '10066099-epel-9-ppc64le', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/htslib /var/lib/copr-rpmbuild/workspace/workdir-5ns7__85/htslib --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-5ns7__85/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-5ns7__85/htslib'... Running: git checkout 7f908d99caaa698e4edc070e538303e597a5ee85 -- cmd: ['git', 'checkout', '7f908d99caaa698e4edc070e538303e597a5ee85', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-5ns7__85/htslib rc: 0 stdout: stderr: Note: switching to '7f908d99caaa698e4edc070e538303e597a5ee85'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 7f908d9 automatic import of htslib Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-5ns7__85/htslib 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 htslib-1.23.tar.bz2 INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o htslib-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/bioinformatics/htslib/htslib-1.23.tar.bz2/md5/686ccffe2ba88ec57d85cca0e3eb2f3a/htslib-1.23.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 4786k 100 4786k 0 0 23.4M 0 --:--:-- --:--:-- --:--:-- 23.4M tail: /var/lib/copr-rpmbuild/main.log: file truncated INFO: Reading stdout from command: md5sum htslib-1.23.tar.bz2 Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-5ns7__85/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-5ns7__85/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769500626.765335 -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-5ns7__85/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-5ns7__85/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769500626.765335 -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-5ns7__85/htslib/htslib.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-1769500626.765335/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-f5b435ad-1314-42a0-8ac8-c0c575841d86 INFO: Checking that bcd7d46e5c0dd1b6fd6f9b44ecfafe2c5f49c1cd180c5fb4b4332203269b1697 image matches host's architecture INFO: Copy content of container bcd7d46e5c0dd1b6fd6f9b44ecfafe2c5f49c1cd180c5fb4b4332203269b1697 to /var/lib/mock/rhel+epel-9-ppc64le-bootstrap-1769500626.765335/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-f5b435ad-1314-42a0-8ac8-c0c575841d86 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-1769500626.765335/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 264 B/s | 258 B 00:00 Red Hat Enterprise Linux - BaseOS 46 MB/s | 59 MB 00:01 Red Hat Enterprise Linux - AppStream 61 MB/s | 71 MB 00:01 Red Hat Enterprise Linux - CodeReady Linux Buil 23 MB/s | 13 MB 00:00 Extra Packages for Enterprise Linux 9 - ppc64le 340 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): basesystem-11-13.el9.noarch.rpm 45 kB/s | 8.0 kB 00:00 (2/211): cracklib-2.9.6-27.el9.ppc64le.rpm 515 kB/s | 100 kB 00:00 (3/211): cpio-2.13-16.el9.ppc64le.rpm 1.4 MB/s | 286 kB 00:00 (4/211): ed-1.14.2-12.el9.ppc64le.rpm 798 kB/s | 81 kB 00:00 (5/211): diffutils-3.7-12.el9.ppc64le.rpm 3.2 MB/s | 417 kB 00:00 (6/211): cracklib-dicts-2.9.6-27.el9.ppc64le.rp 18 MB/s | 3.6 MB 00:00 (7/211): grep-3.6-5.el9.ppc64le.rpm 3.1 MB/s | 281 kB 00:00 (8/211): gawk-5.1.0-6.el9.ppc64le.rpm 8.2 MB/s | 1.0 MB 00:00 (9/211): groff-base-1.22.4-10.el9.ppc64le.rpm 9.8 MB/s | 1.1 MB 00:00 (10/211): info-6.7-15.el9.ppc64le.rpm 2.7 MB/s | 256 kB 00:00 (11/211): json-c-0.14-11.el9.ppc64le.rpm 570 kB/s | 48 kB 00:00 (12/211): libattr-2.5.1-3.el9.ppc64le.rpm 243 kB/s | 21 kB 00:00 (13/211): libcap-ng-0.8.2-7.el9.ppc64le.rpm 433 kB/s | 37 kB 00:00 (14/211): libgpg-error-1.42-5.el9.ppc64le.rpm 2.6 MB/s | 229 kB 00:00 (15/211): libpsl-0.21.1-5.el9.ppc64le.rpm 763 kB/s | 68 kB 00:00 (16/211): libpwquality-1.4.4-8.el9.ppc64le.rpm 1.4 MB/s | 125 kB 00:00 (17/211): libidn2-2.3.0-7.el9.ppc64le.rpm 1.0 MB/s | 108 kB 00:00 (18/211): libsigsegv-2.13-4.el9.ppc64le.rpm 359 kB/s | 31 kB 00:00 (19/211): libunistring-0.9.10-15.el9.ppc64le.rp 5.4 MB/s | 507 kB 00:00 (20/211): libutempter-1.2.1-6.el9.ppc64le.rpm 290 kB/s | 30 kB 00:00 (21/211): libverto-0.3.2-3.el9.ppc64le.rpm 308 kB/s | 25 kB 00:00 (22/211): libxcrypt-4.4.18-3.el9.ppc64le.rpm 1.5 MB/s | 133 kB 00:00 (23/211): lz4-libs-1.9.3-5.el9.ppc64le.rpm 834 kB/s | 88 kB 00:00 (24/211): mpfr-4.1.0-7.el9.ppc64le.rpm 3.5 MB/s | 324 kB 00:00 (25/211): popt-1.18-8.el9.ppc64le.rpm 858 kB/s | 73 kB 00:00 (26/211): publicsuffix-list-dafsa-20210518-3.el 695 kB/s | 59 kB 00:00 (27/211): readline-8.1-4.el9.ppc64le.rpm 2.5 MB/s | 231 kB 00:00 (28/211): sed-4.8-9.el9.ppc64le.rpm 3.5 MB/s | 315 kB 00:00 (29/211): xz-5.2.5-8.el9_0.ppc64le.rpm 2.5 MB/s | 238 kB 00:00 (30/211): xz-libs-5.2.5-8.el9_0.ppc64le.rpm 1.3 MB/s | 117 kB 00:00 (31/211): gzip-1.12-1.el9.ppc64le.rpm 2.0 MB/s | 172 kB 00:00 (32/211): keyutils-libs-1.6.3-1.el9.ppc64le.rpm 318 kB/s | 35 kB 00:00 (33/211): libpkgconf-1.7.3-10.el9.ppc64le.rpm 490 kB/s | 42 kB 00:00 (34/211): pkgconf-1.7.3-10.el9.ppc64le.rpm 393 kB/s | 45 kB 00:00 (35/211): pkgconf-pkg-config-1.7.3-10.el9.ppc64 136 kB/s | 12 kB 00:00 (36/211): pkgconf-m4-1.7.3-10.el9.noarch.rpm 143 kB/s | 16 kB 00:00 (37/211): zip-3.0-35.el9.ppc64le.rpm 2.9 MB/s | 276 kB 00:00 (38/211): gmp-6.2.0-13.el9.ppc64le.rpm 3.4 MB/s | 305 kB 00:00 (39/211): libffi-3.4.2-8.el9.ppc64le.rpm 462 kB/s | 40 kB 00:00 (40/211): lua-libs-5.4.4-4.el9.ppc64le.rpm 1.2 MB/s | 149 kB 00:00 (41/211): zlib-1.2.11-40.el9.ppc64le.rpm 1.1 MB/s | 104 kB 00:00 (42/211): bash-5.1.8-9.el9.ppc64le.rpm 15 MB/s | 1.7 MB 00:00 (43/211): file-5.39-16.el9.ppc64le.rpm 483 kB/s | 52 kB 00:00 (44/211): file-libs-5.39-16.el9.ppc64le.rpm 5.9 MB/s | 604 kB 00:00 (45/211): setup-2.13.7-10.el9.noarch.rpm 1.5 MB/s | 150 kB 00:00 (46/211): libacl-2.3.1-4.el9.ppc64le.rpm 146 kB/s | 26 kB 00:00 (47/211): libevent-2.1.12-8.el9_4.ppc64le.rpm 2.7 MB/s | 281 kB 00:00 (48/211): bzip2-1.0.8-10.el9_5.ppc64le.rpm 638 kB/s | 60 kB 00:00 (49/211): bzip2-libs-1.0.8-10.el9_5.ppc64le.rpm 471 kB/s | 46 kB 00:00 (50/211): filesystem-3.16-5.el9.ppc64le.rpm 29 MB/s | 4.8 MB 00:00 (51/211): findutils-4.8.0-7.el9.ppc64le.rpm 6.2 MB/s | 589 kB 00:00 (52/211): gdbm-libs-1.23-1.el9.ppc64le.rpm 654 kB/s | 64 kB 00:00 (53/211): libbrotli-1.0.9-7.el9_5.ppc64le.rpm 2.8 MB/s | 339 kB 00:00 (54/211): libeconf-0.4.1-4.el9.ppc64le.rpm 283 kB/s | 32 kB 00:00 (55/211): libgcrypt-1.10.0-11.el9.ppc64le.rpm 4.9 MB/s | 599 kB 00:00 (56/211): libnghttp2-1.43.0-6.el9.ppc64le.rpm 969 kB/s | 84 kB 00:00 (57/211): librtas-2.0.6-1.el9.ppc64le.rpm 1.0 MB/s | 84 kB 00:00 (58/211): p11-kit-0.25.3-3.el9_5.ppc64le.rpm 5.7 MB/s | 535 kB 00:00 (59/211): p11-kit-trust-0.25.3-3.el9_5.ppc64le. 1.8 MB/s | 157 kB 00:00 (60/211): pcre-8.44-4.el9.ppc64le.rpm 2.2 MB/s | 203 kB 00:00 (61/211): pcre2-10.40-6.el9.ppc64le.rpm 2.7 MB/s | 237 kB 00:00 (62/211): alternatives-1.24-2.el9.ppc64le.rpm 408 kB/s | 43 kB 00:00 (63/211): pcre2-syntax-10.40-6.el9.noarch.rpm 1.3 MB/s | 144 kB 00:00 (64/211): coreutils-common-8.32-39.el9.ppc64le. 17 MB/s | 2.0 MB 00:00 (65/211): libfdisk-2.37.4-21.el9.ppc64le.rpm 1.9 MB/s | 170 kB 00:00 (66/211): libmount-2.37.4-21.el9.ppc64le.rpm 1.7 MB/s | 153 kB 00:00 (67/211): libselinux-3.6-3.el9.ppc64le.rpm 1.1 MB/s | 100 kB 00:00 (68/211): libsemanage-3.6-5.el9_6.ppc64le.rpm 1.5 MB/s | 133 kB 00:00 (69/211): libsmartcols-2.37.4-21.el9.ppc64le.rp 795 kB/s | 70 kB 00:00 (70/211): libtool-ltdl-2.4.6-46.el9.ppc64le.rpm 467 kB/s | 41 kB 00:00 (71/211): libzstd-1.5.5-1.el9.ppc64le.rpm 3.4 MB/s | 322 kB 00:00 (72/211): openldap-2.6.8-4.el9.ppc64le.rpm 3.4 MB/s | 322 kB 00:00 (73/211): util-linux-2.37.4-21.el9.ppc64le.rpm 19 MB/s | 2.3 MB 00:00 (74/211): zstd-1.5.5-1.el9.ppc64le.rpm 3.7 MB/s | 407 kB 00:00 (75/211): util-linux-core-2.37.4-21.el9.ppc64le 4.1 MB/s | 488 kB 00:00 (76/211): coreutils-8.32-39.el9.ppc64le.rpm 11 MB/s | 1.2 MB 00:00 (77/211): krb5-libs-1.21.1-8.el9_6.ppc64le.rpm 7.1 MB/s | 846 kB 00:00 (78/211): libblkid-2.37.4-21.el9.ppc64le.rpm 1.1 MB/s | 125 kB 00:00 (79/211): libdb-5.3.28-57.el9_6.ppc64le.rpm 8.2 MB/s | 817 kB 00:00 (80/211): libtasn1-4.16.0-9.el9.ppc64le.rpm 954 kB/s | 82 kB 00:00 (81/211): libuuid-2.37.4-21.el9.ppc64le.rpm 372 kB/s | 32 kB 00:00 (82/211): libarchive-3.5.3-6.el9_6.ppc64le.rpm 4.7 MB/s | 454 kB 00:00 (83/211): which-2.21-30.el9_6.ppc64le.rpm 441 kB/s | 42 kB 00:00 (84/211): pam-1.5.1-26.el9_6.ppc64le.rpm 6.1 MB/s | 662 kB 00:00 (85/211): audit-libs-3.1.5-7.el9.ppc64le.rpm 1.5 MB/s | 137 kB 00:00 (86/211): crypto-policies-20250905-1.git377cc42 1.0 MB/s | 90 kB 00:00 (87/211): curl-7.76.1-34.el9.ppc64le.rpm 3.3 MB/s | 295 kB 00:00 (88/211): cyrus-sasl-lib-2.1.27-22.el9.ppc64le. 8.5 MB/s | 856 kB 00:00 (89/211): elfutils-default-yama-scope-0.193-1.e 111 kB/s | 9.7 kB 00:00 (90/211): elfutils-debuginfod-client-0.193-1.el 327 kB/s | 46 kB 00:00 (91/211): elfutils-0.193-1.el9.ppc64le.rpm 3.7 MB/s | 601 kB 00:00 (92/211): elfutils-libs-0.193-1.el9.ppc64le.rpm 3.3 MB/s | 305 kB 00:00 (93/211): libcap-2.48-10.el9.ppc64le.rpm 720 kB/s | 74 kB 00:00 (94/211): elfutils-libelf-0.193-1.el9.ppc64le.r 1.8 MB/s | 211 kB 00:00 (95/211): libcom_err-1.46.5-8.el9.ppc64le.rpm 290 kB/s | 27 kB 00:00 (96/211): libcurl-7.76.1-34.el9.ppc64le.rpm 3.4 MB/s | 314 kB 00:00 (97/211): libgcc-11.5.0-11.el9.ppc64le.rpm 743 kB/s | 74 kB 00:00 (98/211): libgomp-11.5.0-11.el9.ppc64le.rpm 3.1 MB/s | 269 kB 00:00 (99/211): libsepol-3.6-3.el9.ppc64le.rpm 2.8 MB/s | 366 kB 00:00 (100/211): libstdc++-11.5.0-11.el9.ppc64le.rpm 6.6 MB/s | 837 kB 00:00 (101/211): ncurses-6.2-12.20210508.el9.ppc64le. 3.8 MB/s | 413 kB 00:00 (102/211): ncurses-base-6.2-12.20210508.el9.noa 1.1 MB/s | 96 kB 00:00 (103/211): ncurses-libs-6.2-12.20210508.el9.ppc 3.5 MB/s | 370 kB 00:00 (104/211): openssl-fips-provider-3.0.7-8.el9.pp 110 kB/s | 9.2 kB 00:00 (105/211): openssl-fips-provider-so-3.0.7-8.el9 5.3 MB/s | 563 kB 00:00 (106/211): rpm-build-libs-4.16.1.3-39.el9.ppc64 966 kB/s | 96 kB 00:00 (107/211): rpm-4.16.1.3-39.el9.ppc64le.rpm 4.3 MB/s | 534 kB 00:00 (108/211): rpm-libs-4.16.1.3-39.el9.ppc64le.rpm 1.9 MB/s | 351 kB 00:00 (109/211): unzip-6.0-59.el9.ppc64le.rpm 1.3 MB/s | 186 kB 00:00 (110/211): shadow-utils-4.9-15.el9.ppc64le.rpm 6.1 MB/s | 1.2 MB 00:00 (111/211): glibc-common-2.34-231.el9_7.2.ppc64l 1.4 MB/s | 323 kB 00:00 (112/211): glibc-2.34-231.el9_7.2.ppc64le.rpm 7.7 MB/s | 2.7 MB 00:00 (113/211): glibc-gconv-extra-2.34-231.el9_7.2.p 5.5 MB/s | 1.7 MB 00:00 (114/211): redhat-release-9.7-0.7.el9.ppc64le.r 561 kB/s | 53 kB 00:00 (115/211): glibc-minimal-langpack-2.34-231.el9_ 95 kB/s | 22 kB 00:00 (116/211): sqlite-libs-3.34.1-9.el9_7.ppc64le.r 7.3 MB/s | 731 kB 00:00 (117/211): ca-certificates-2025.2.80_v9.0.305-9 9.2 MB/s | 1.0 MB 00:00 (118/211): systemd-libs-252-55.el9_7.7.ppc64le. 6.6 MB/s | 708 kB 00:00 (119/211): libxml2-2.9.13-14.el9_7.ppc64le.rpm 5.7 MB/s | 823 kB 00:00 (120/211): tzdata-2025c-1.el9.noarch.rpm 8.8 MB/s | 904 kB 00:00 (121/211): libssh-0.10.4-17.el9_7.ppc64le.rpm 2.5 MB/s | 238 kB 00:00 (122/211): libssh-config-0.10.4-17.el9_7.noarch 92 kB/s | 8.1 kB 00:00 (123/211): binutils-gold-2.35.2-67.el9_7.1.ppc6 9.4 MB/s | 1.0 MB 00:00 (124/211): tar-1.34-9.el9_7.ppc64le.rpm 8.5 MB/s | 916 kB 00:00 (125/211): binutils-2.35.2-67.el9_7.1.ppc64le.r 28 MB/s | 5.0 MB 00:00 (126/211): openssl-3.5.1-5.el9_7.ppc64le.rpm 11 MB/s | 1.5 MB 00:00 (127/211): openssl-libs-3.5.1-5.el9_7.ppc64le.r 18 MB/s | 2.4 MB 00:00 (128/211): perl-Encode-3.08-462.el9.ppc64le.rpm 13 MB/s | 1.7 MB 00:00 (129/211): perl-Exporter-5.74-461.el9.noarch.rp 375 kB/s | 34 kB 00:00 (130/211): perl-File-Temp-0.231.100-4.el9.noarc 741 kB/s | 63 kB 00:00 (131/211): perl-MIME-Base64-3.16-4.el9.ppc64le. 404 kB/s | 35 kB 00:00 (132/211): perl-Mozilla-CA-20200520-6.el9.noarc 154 kB/s | 14 kB 00:00 (133/211): perl-Socket-2.031-4.el9.ppc64le.rpm 685 kB/s | 59 kB 00:00 (134/211): perl-Term-Cap-1.17-460.el9.noarch.rp 278 kB/s | 24 kB 00:00 (135/211): perl-Time-Local-1.300-7.el9.noarch.r 425 kB/s | 37 kB 00:00 (136/211): perl-parent-0.238-460.el9.noarch.rpm 190 kB/s | 16 kB 00:00 (137/211): perl-srpm-macros-1-41.el9.noarch.rpm 109 kB/s | 9.4 kB 00:00 (138/211): ghc-srpm-macros-1.5.0-6.el9.noarch.r 103 kB/s | 9.0 kB 00:00 (139/211): rust-srpm-macros-17-4.el9.noarch.rpm 102 kB/s | 11 kB 00:00 (140/211): lua-srpm-macros-1-6.el9.noarch.rpm 117 kB/s | 10 kB 00:00 (141/211): perl-Digest-MD5-2.58-4.el9.ppc64le.r 442 kB/s | 40 kB 00:00 (142/211): patch-2.7.6-16.el9.ppc64le.rpm 1.2 MB/s | 140 kB 00:00 (143/211): perl-IO-Socket-IP-0.41-5.el9.noarch. 419 kB/s | 45 kB 00:00 (144/211): perl-Pod-Escapes-1.07-460.el9.noarch 262 kB/s | 22 kB 00:00 (145/211): perl-Pod-Simple-3.42-4.el9.noarch.rp 2.3 MB/s | 229 kB 00:00 (146/211): perl-Term-ANSIColor-5.01-461.el9.noa 470 kB/s | 51 kB 00:00 (147/211): perl-Text-ParseWords-3.30-460.el9.no 205 kB/s | 18 kB 00:00 (148/211): perl-Text-Tabs+Wrap-2013.0523-460.el 277 kB/s | 25 kB 00:00 (149/211): perl-URI-5.09-3.el9.noarch.rpm 1.3 MB/s | 125 kB 00:00 (150/211): perl-constant-1.33-461.el9.noarch.rp 292 kB/s | 25 kB 00:00 (151/211): openblas-srpm-macros-2-11.el9.noarch 89 kB/s | 8.6 kB 00:00 (152/211): perl-Data-Dumper-2.174-462.el9.ppc64 678 kB/s | 59 kB 00:00 (153/211): perl-File-Path-2.18-4.el9.noarch.rpm 430 kB/s | 38 kB 00:00 (154/211): perl-Pod-Usage-2.01-4.el9.noarch.rpm 484 kB/s | 43 kB 00:00 (155/211): perl-libnet-3.13-4.el9.noarch.rpm 1.4 MB/s | 134 kB 00:00 (156/211): perl-Pod-Perldoc-3.28.01-461.el9.noa 614 kB/s | 92 kB 00:00 (157/211): perl-podlators-4.14-460.el9.noarch.r 1.2 MB/s | 118 kB 00:00 (158/211): fonts-srpm-macros-2.0.5-7.el9.1.noar 319 kB/s | 29 kB 00:00 (159/211): ocaml-srpm-macros-6-6.el9.noarch.rpm 100 kB/s | 9.1 kB 00:00 (160/211): perl-Carp-1.50-460.el9.noarch.rpm 349 kB/s | 31 kB 00:00 (161/211): perl-Digest-1.19-4.el9.noarch.rpm 319 kB/s | 29 kB 00:00 (162/211): perl-Getopt-Long-2.52-4.el9.noarch.r 614 kB/s | 64 kB 00:00 (163/211): perl-Storable-3.21-460.el9.ppc64le.r 1.1 MB/s | 101 kB 00:00 (164/211): perl-PathTools-3.78-461.el9.ppc64le. 1.0 MB/s | 93 kB 00:00 (165/211): qt5-srpm-macros-5.15.9-1.el9.noarch. 96 kB/s | 9.1 kB 00:00 (166/211): perl-HTTP-Tiny-0.076-462.el9.noarch. 631 kB/s | 57 kB 00:00 (167/211): perl-Scalar-List-Utils-1.56-462.el9. 864 kB/s | 78 kB 00:00 (168/211): perl-IO-Socket-SSL-2.073-2.el9.noarc 2.4 MB/s | 221 kB 00:00 (169/211): pyproject-srpm-macros-1.16.2-1.el9.n 166 kB/s | 14 kB 00:00 (170/211): python-srpm-macros-3.9-54.el9.noarch 153 kB/s | 18 kB 00:00 (171/211): perl-AutoLoader-5.74-481.1.el9_6.noa 193 kB/s | 21 kB 00:00 (172/211): perl-B-1.80-481.1.el9_6.ppc64le.rpm 1.5 MB/s | 183 kB 00:00 (173/211): perl-Class-Struct-0.66-481.1.el9_6.n 243 kB/s | 22 kB 00:00 (174/211): perl-Errno-1.30-481.1.el9_6.ppc64le. 142 kB/s | 14 kB 00:00 (175/211): perl-File-Basename-2.85-481.1.el9_6. 142 kB/s | 17 kB 00:00 (176/211): perl-Fcntl-1.13-481.1.el9_6.ppc64le. 168 kB/s | 20 kB 00:00 (177/211): perl-File-stat-1.09-481.1.el9_6.noar 180 kB/s | 17 kB 00:00 (178/211): perl-FileHandle-2.03-481.1.el9_6.noa 146 kB/s | 15 kB 00:00 (179/211): perl-Getopt-Std-1.12-481.1.el9_6.noa 143 kB/s | 15 kB 00:00 (180/211): perl-IO-1.43-481.1.el9_6.ppc64le.rpm 600 kB/s | 89 kB 00:00 (181/211): perl-IPC-Open3-1.21-481.1.el9_6.noar 194 kB/s | 22 kB 00:00 (182/211): perl-POSIX-1.94-481.1.el9_6.ppc64le. 860 kB/s | 98 kB 00:00 (183/211): perl-SelectSaver-1.02-481.1.el9_6.no 84 kB/s | 11 kB 00:00 (184/211): perl-Symbol-1.08-481.1.el9_6.noarch. 120 kB/s | 14 kB 00:00 (185/211): perl-base-2.27-481.1.el9_6.noarch.rp 138 kB/s | 16 kB 00:00 (186/211): perl-if-0.60.800-481.1.el9_6.noarch. 149 kB/s | 14 kB 00:00 (187/211): perl-interpreter-5.32.1-481.1.el9_6. 714 kB/s | 70 kB 00:00 (188/211): perl-mro-1.23-481.1.el9_6.ppc64le.rp 284 kB/s | 28 kB 00:00 (189/211): perl-libs-5.32.1-481.1.el9_6.ppc64le 14 MB/s | 2.3 MB 00:00 (190/211): perl-overload-1.31-481.1.el9_6.noarc 440 kB/s | 45 kB 00:00 (191/211): perl-overloading-0.02-481.1.el9_6.no 105 kB/s | 12 kB 00:00 (192/211): perl-subs-1.03-481.1.el9_6.noarch.rp 101 kB/s | 11 kB 00:00 (193/211): perl-vars-1.05-481.1.el9_6.noarch.rp 125 kB/s | 13 kB 00:00 (194/211): efi-srpm-macros-6-4.el9.noarch.rpm 163 kB/s | 21 kB 00:00 (195/211): redhat-rpm-config-210-1.el9.noarch.r 616 kB/s | 70 kB 00:00 (196/211): gdb-minimal-16.3-2.el9.ppc64le.rpm 27 MB/s | 4.6 MB 00:00 (197/211): rpm-build-4.16.1.3-39.el9.ppc64le.rp 750 kB/s | 67 kB 00:00 (198/211): debugedit-5.0-11.el9.ppc64le.rpm 929 kB/s | 81 kB 00:00 (199/211): dwz-0.16-1.el9.ppc64le.rpm 1.1 MB/s | 140 kB 00:00 (200/211): kernel-srpm-macros-1.0-14.el9.noarch 121 kB/s | 14 kB 00:00 (201/211): perl-Net-SSLeay-1.94-3.el9.ppc64le.r 3.3 MB/s | 423 kB 00:00 (202/211): go-srpm-macros-3.6.0-12.el9_7.noarch 211 kB/s | 27 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] [MIRROR] ansible-srpm-macros-1-16.el9.noarch.rpm: Curl error (28): Timeout was reached for http://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 80: Connection timed out] [MIRROR] epel-rpm-macros-9-17.el9.noarch.rpm: Curl error (28): Timeout was reached for http://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 80: Connection timed out] [MIRROR] forge-srpm-macros-0.4.0-1.el9.noarch.rpm: Curl error (28): Timeout was reached for http://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 80: Connection timed out] (203/211): epel-rpm-macros-9-17.el9.noarch.rpm 261 B/s | 15 kB 00:58 (204/211): forge-srpm-macros-0.4.0-1.el9.noarch 339 B/s | 19 kB 00:58 (205/211): ghc-srpm-macros-epel-1.9.1-1.el9.noa 34 kB/s | 7.5 kB 00:00 (206/211): fpc-srpm-macros-1.3-7.el9.noarch.rpm 28 kB/s | 7.5 kB 00:00 (207/211): qt6-srpm-macros-6.6.2-1.el9.noarch.r 36 kB/s | 8.7 kB 00:00 (208/211): go-srpm-macros-epel-3.8.0-1.el9.noar 62 kB/s | 26 kB 00:00 (209/211): rpmautospec-rpm-macros-0.8.1-11.el9. 45 kB/s | 11 kB 00:00 (210/211): rust-srpm-macros-epel-26.3-1.el9.noa 48 kB/s | 10 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] (211/211): ansible-srpm-macros-1-16.el9.noarch. 241 B/s | 21 kB 01:27 -------------------------------------------------------------------------------- Total 791 kB/s | 73 MB 01:34 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/htslib-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-1769500626.765335/root/var/log/dnf.rpm.log /var/lib/mock/rhel+epel-9-ppc64le-1769500626.765335/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-9-ppc64le-1769500626.765335/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-5ns7__85/htslib/htslib.spec) Config(child) 4 minutes 31 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/htslib-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-1769500626.765335/root. INFO: reusing tmpfs at /var/lib/mock/rhel+epel-9-ppc64le-bootstrap-1769500626.765335/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-1769500626.765335/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 htslib-1.23-1.el9.src.rpm Start: build setup for htslib-1.23-1.el9.src.rpm Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1769040000 Wrote: /builddir/build/SRPMS/htslib-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 5.3 kB/s | 1.5 kB 00:00 Red Hat Enterprise Linux - BaseOS 11 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux - AppStream 30 kB/s | 4.5 kB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 33 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 9 - ppc64le 1.4 MB/s | 66 kB 00:00 Package perl-Data-Dumper-2.174-462.el9.ppc64le is already installed. 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: bzip2-devel ppc64le 1.0.8-10.el9_5 appstream 215 k gcc ppc64le 11.5.0-11.el9 appstream 28 M libcurl-devel ppc64le 7.76.1-34.el9 appstream 974 k make ppc64le 1:4.3-8.el9 baseos 554 k openssl-devel ppc64le 1:3.5.1-5.el9_7 appstream 4.8 M perl-FindBin noarch 1.51-481.1.el9_6 appstream 14 k perl-lib ppc64le 0.65-481.1.el9_6 appstream 14 k xz-devel ppc64le 5.2.5-8.el9_0 appstream 59 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 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 Transaction Summary ================================================================================ Install 22 Packages Total download size: 79 M Installed size: 258 M Downloading Packages: (1/22): libedit-3.1-38.20210216cvs.el9.ppc64le. 792 kB/s | 119 kB 00:00 (2/22): make-4.3-8.el9.ppc64le.rpm 2.9 MB/s | 554 kB 00:00 (3/22): libatomic-11.5.0-11.el9.ppc64le.rpm 130 kB/s | 24 kB 00:00 (4/22): libmpc-1.2.1-4.el9.ppc64le.rpm 786 kB/s | 70 kB 00:00 (5/22): libxcrypt-devel-4.4.18-3.el9.ppc64le.rp 332 kB/s | 32 kB 00:00 (6/22): xz-devel-5.2.5-8.el9_0.ppc64le.rpm 532 kB/s | 59 kB 00:00 (7/22): zlib-devel-1.2.11-40.el9.ppc64le.rpm 556 kB/s | 47 kB 00:00 (8/22): bzip2-devel-1.0.8-10.el9_5.ppc64le.rpm 2.4 MB/s | 215 kB 00:00 (9/22): perl-lib-0.65-481.1.el9_6.ppc64le.rpm 167 kB/s | 14 kB 00:00 (10/22): perl-FindBin-1.51-481.1.el9_6.noarch.r 116 kB/s | 14 kB 00:00 (11/22): gcc-plugin-annobin-11.5.0-11.el9.ppc64 440 kB/s | 39 kB 00:00 (12/22): cpp-11.5.0-11.el9.ppc64le.rpm 40 MB/s | 9.2 MB 00:00 (13/22): annobin-12.98-1.el9.ppc64le.rpm 7.7 MB/s | 1.1 MB 00:00 (14/22): libasan-11.5.0-11.el9.ppc64le.rpm 4.5 MB/s | 430 kB 00:00 (15/22): libcurl-devel-7.76.1-34.el9.ppc64le.rp 9.3 MB/s | 974 kB 00:00 (16/22): libubsan-11.5.0-11.el9.ppc64le.rpm 1.8 MB/s | 197 kB 00:00 (17/22): llvm-libs-20.1.8-3.el9.ppc64le.rpm 42 MB/s | 30 MB 00:00 (18/22): llvm-filesystem-20.1.8-3.el9.ppc64le.r 50 kB/s | 9.1 kB 00:00 (19/22): gcc-11.5.0-11.el9.ppc64le.rpm 40 MB/s | 28 MB 00:00 (20/22): glibc-devel-2.34-231.el9_7.2.ppc64le.r 3.2 MB/s | 569 kB 00:00 (21/22): openssl-devel-3.5.1-5.el9_7.ppc64le.rp 21 MB/s | 4.8 MB 00:00 (22/22): kernel-headers-5.14.0-611.26.1.el9_7.p 23 MB/s | 2.9 MB 00:00 -------------------------------------------------------------------------------- Total 56 MB/s | 79 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-4.el9.ppc64le 1/22 Installing : cpp-11.5.0-11.el9.ppc64le 2/22 Installing : kernel-headers-5.14.0-611.26.1.el9_7.ppc64le 3/22 Installing : glibc-devel-2.34-231.el9_7.2.ppc64le 4/22 Installing : libxcrypt-devel-4.4.18-3.el9.ppc64le 5/22 Installing : llvm-filesystem-20.1.8-3.el9.ppc64le 6/22 Installing : libubsan-11.5.0-11.el9.ppc64le 7/22 Installing : libasan-11.5.0-11.el9.ppc64le 8/22 Installing : libatomic-11.5.0-11.el9.ppc64le 9/22 Installing : make-1:4.3-8.el9.ppc64le 10/22 Installing : gcc-11.5.0-11.el9.ppc64le 11/22 Running scriptlet: gcc-11.5.0-11.el9.ppc64le 11/22 Installing : libedit-3.1-38.20210216cvs.el9.ppc64le 12/22 Installing : llvm-libs-20.1.8-3.el9.ppc64le 13/22 Installing : annobin-12.98-1.el9.ppc64le 14/22 Running scriptlet: annobin-12.98-1.el9.ppc64le 14/22 Installing : gcc-plugin-annobin-11.5.0-11.el9.ppc64le 15/22 Running scriptlet: gcc-plugin-annobin-11.5.0-11.el9.ppc64le 15/22 Installing : openssl-devel-1:3.5.1-5.el9_7.ppc64le 16/22 Installing : libcurl-devel-7.76.1-34.el9.ppc64le 17/22 Installing : perl-lib-0.65-481.1.el9_6.ppc64le 18/22 Installing : perl-FindBin-1.51-481.1.el9_6.noarch 19/22 Installing : bzip2-devel-1.0.8-10.el9_5.ppc64le 20/22 Installing : zlib-devel-1.2.11-40.el9.ppc64le 21/22 Installing : xz-devel-5.2.5-8.el9_0.ppc64le 22/22 Running scriptlet: xz-devel-5.2.5-8.el9_0.ppc64le 22/22 Verifying : libedit-3.1-38.20210216cvs.el9.ppc64le 1/22 Verifying : make-1:4.3-8.el9.ppc64le 2/22 Verifying : libatomic-11.5.0-11.el9.ppc64le 3/22 Verifying : libmpc-1.2.1-4.el9.ppc64le 4/22 Verifying : libxcrypt-devel-4.4.18-3.el9.ppc64le 5/22 Verifying : xz-devel-5.2.5-8.el9_0.ppc64le 6/22 Verifying : zlib-devel-1.2.11-40.el9.ppc64le 7/22 Verifying : bzip2-devel-1.0.8-10.el9_5.ppc64le 8/22 Verifying : perl-FindBin-1.51-481.1.el9_6.noarch 9/22 Verifying : perl-lib-0.65-481.1.el9_6.ppc64le 10/22 Verifying : cpp-11.5.0-11.el9.ppc64le 11/22 Verifying : gcc-plugin-annobin-11.5.0-11.el9.ppc64le 12/22 Verifying : llvm-libs-20.1.8-3.el9.ppc64le 13/22 Verifying : annobin-12.98-1.el9.ppc64le 14/22 Verifying : gcc-11.5.0-11.el9.ppc64le 15/22 Verifying : libasan-11.5.0-11.el9.ppc64le 16/22 Verifying : libcurl-devel-7.76.1-34.el9.ppc64le 17/22 Verifying : libubsan-11.5.0-11.el9.ppc64le 18/22 Verifying : llvm-filesystem-20.1.8-3.el9.ppc64le 19/22 Verifying : glibc-devel-2.34-231.el9_7.2.ppc64le 20/22 Verifying : openssl-devel-1:3.5.1-5.el9_7.ppc64le 21/22 Verifying : kernel-headers-5.14.0-611.26.1.el9_7.ppc64le 22/22 Installed products updated. Installed: annobin-12.98-1.el9.ppc64le bzip2-devel-1.0.8-10.el9_5.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 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 libcurl-devel-7.76.1-34.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 openssl-devel-1:3.5.1-5.el9_7.ppc64le perl-FindBin-1.51-481.1.el9_6.noarch perl-lib-0.65-481.1.el9_6.ppc64le xz-devel-5.2.5-8.el9_0.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/htslib-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 6.2 kB/s | 1.5 kB 00:00 Red Hat Enterprise Linux - BaseOS 798 B/s | 4.1 kB 00:05 Red Hat Enterprise Linux - AppStream 1.3 kB/s | 4.5 kB 00:03 Red Hat Enterprise Linux - CodeReady Linux Buil 29 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 9 - ppc64le 1.6 MB/s | 66 kB 00:00 Package bzip2-devel-1.0.8-10.el9_5.ppc64le is already installed. Package gcc-11.5.0-11.el9.ppc64le is already installed. Package libcurl-devel-7.76.1-34.el9.ppc64le is already installed. Package make-1:4.3-8.el9.ppc64le is already installed. Package openssl-devel-1:3.5.1-5.el9_7.ppc64le is already installed. Package perl-Data-Dumper-2.174-462.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 xz-devel-5.2.5-8.el9_0.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 htslib-1.23-1.el9.src.rpm Start: rpmbuild htslib-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.zRlf6I + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf htslib-1.23 + /usr/bin/bzip2 -dc /builddir/build/SOURCES/htslib-1.23.tar.bz2 + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd htslib-1.23 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.6uZEn1 + umask 022 + cd /builddir/build/BUILD + cd htslib-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' ./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 ./config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./config.guess ++ basename ./config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess '/usr/lib/rpm/redhat/config.guess' -> './config.guess' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub '/usr/lib/rpm/redhat/config.sub' -> './config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh + ./configure --build=powerpc64le-redhat-linux-gnu --host=powerpc64le-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking 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 powerpc64le-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for powerpc64le-redhat-linux-gnu-pkg-config... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed checking shared library type for powerpc64le-redhat-linux-gnu... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... powerpc64le-redhat-linux-gnu checking host system type... powerpc64le-redhat-linux-gnu checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes checking for library containing dlsym... none required checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for fstatat... yes checking for CMSG_LEN... yes checking for epoll... yes (edge triggered) checking for sendfile... yes, Linux-style checking whether EHOSTDOWN is declared... yes checking whether ENONET is declared... yes checking whether AI_V4MAPPED is declared... yes checking whether AI_ADDRCONFIG is declared... yes checking whether the compiler accepts -Wextra... yes checking whether the compiler accepts -Wformat... yes checking whether the compiler accepts -Wformat=2... yes checking whether the compiler accepts -Wconversion... yes checking whether the compiler accepts -Wtrampolines... yes checking whether the compiler accepts -Wstrict-aliasing... yes checking whether the compiler accepts -fstack-clash-protection... yes checking whether the compiler accepts -fstack-protector-strong... yes checking whether the compiler accepts -fcf-protection=full... no checking whether the compiler accepts -mbranch-protection=standard... no checking whether the compiler accepts -fno-delete-null-pointer-checks... yes checking whether the compiler accepts -Wl,-z,noexecstack... yes checking whether the compiler accepts -Wl,-z,relro... yes checking whether the compiler accepts -Wl,-z,now... yes checking whether the compiler accepts -Wl,--as-needed... yes checking whether the compiler accepts -Wl,--no-copy-dt-needed-entries... yes checking whether the compiler accepts -Wl,-z,nodlopen... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk configure: WARNING: unrecognized options: --disable-dependency-tracking + /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 -fvisibility=hidden -I. -c -o kfunc.o kfunc.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 -fvisibility=hidden -I. -c -o errmod.o errmod.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 -fvisibility=hidden -I. -c -o kstring.o kstring.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 -fvisibility=hidden -I. -c -o faidx.o faidx.c echo '#define HTS_VERSION_TEXT "1.23"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ '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 -fvisibility=hidden' \ '-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 -fvisibility=hidden -rdynamic' \ '-llzma -lbz2 -lz -lm ' > config_vars.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 -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_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 -fvisibility=hidden -I. -c -o hfile.o hfile.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 -fvisibility=hidden -I. -c -o hts_os.o hts_os.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 -fvisibility=hidden -I. -c -o bgzf.o bgzf.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 -fvisibility=hidden -I. -c -o md5.o md5.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 -fvisibility=hidden -I. -c -o multipart.o multipart.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 -fvisibility=hidden -I. -c -o probaln.o probaln.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 -fvisibility=hidden -I. -c -o realn.o realn.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 -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.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 -fvisibility=hidden -I. -c -o region.o region.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 -fvisibility=hidden -I. -c -o simd.o simd.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 -fvisibility=hidden -I. -c -o regidx.o regidx.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 -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.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 -fvisibility=hidden -I. -c -o sam_mods.o sam_mods.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 -fvisibility=hidden -I. -c -o textutils.o textutils.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 -fvisibility=hidden -I. -c -o tbx.o tbx.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 -fvisibility=hidden -I. -c -o header.o header.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 -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.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 -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.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 -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.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 -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.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 -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.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 -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.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 -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_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 -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_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 -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.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 -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_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 -fvisibility=hidden -I. -c -o sam.o sam.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 -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.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 -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.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 -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.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 -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/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 -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -c -o plugin.o plugin.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.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 -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.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 -fvisibility=hidden -I. -c -o vcf.o vcf.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 -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.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 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.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 -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.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 -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_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 -fvisibility=hidden -I. -fpic -c -o faidx.pico 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 -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.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 -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.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 -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.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 -fvisibility=hidden -I. -fpic -c -o md5.pico md5.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 -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.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 -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.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 -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.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 -fvisibility=hidden -I. -fpic -c -o realn.pico realn.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 -fvisibility=hidden -I. -fpic -c -o region.pico region.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 -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.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 -fvisibility=hidden -I. -fpic -c -o simd.pico simd.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 -fvisibility=hidden -I. -fpic -c -o sam_mods.pico sam_mods.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 -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.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 -fvisibility=hidden -I. -fpic -c -o header.pico header.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 -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.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 -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.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 -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.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 -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.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 -fvisibility=hidden -I. -fpic -c -o hts.pico hts.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 -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.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 -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.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 -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.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 -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.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 -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_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 -fvisibility=hidden -I. -fpic -c -o sam.pico sam.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 -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_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 -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.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 -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.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 -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.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 -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_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 -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.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 -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.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 -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/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 -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.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 -fvisibility=hidden -I. -c -o htsfile.o htsfile.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 -fvisibility=hidden -I. -c -o bgzip.o bgzip.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 -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.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 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.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 -fvisibility=hidden -I. -c -o tabix.o tabix.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 -fvisibility=hidden -I. -c -o annot-tsv.o annot-tsv.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 -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.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 -fvisibility=hidden -I. -c -o test/pileup.o test/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 -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.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 -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.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 -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.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 -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.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 -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.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 -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.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 -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.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 -fvisibility=hidden -I. -c -o test/test_faidx.o test/test_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 -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.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 -fvisibility=hidden -I. -c -o test/test_khash.o test/test_khash.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 -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.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 -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.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 -fvisibility=hidden -I. -c -o test/test_nibbles.o test/test_nibbles.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 -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.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 -fvisibility=hidden -I. -c -o test/test_time_funcs.o test/test_time_funcs.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 -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.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 -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.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 -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.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 -fvisibility=hidden -I. -c -o test/sam.o test/sam.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 -fvisibility=hidden -I. -c -o test/test_index.o test/test_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 -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.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 -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.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 -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power9 -mtune=power9 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_view.o test/test_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 -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk 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 -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > htslib-uninstalled.pc 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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.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 -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/listener.o ref_cache/listener.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/log_files.o ref_cache/log_files.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/misc.o ref_cache/misc.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 -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/ping.o ref_cache/ping.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/http_parser.o ref_cache/http_parser.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/request_handler.o ref_cache/request_handler.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/ref_files.o ref_cache/ref_files.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/main.o ref_cache/main.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/transaction.o ref_cache/transaction.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/server.o ref_cache/server.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/upstream.o ref_cache/upstream.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 -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm 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 -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o 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 -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm 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 -fvisibility=hidden -rdynamic -Wl,-z,noexecstack -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,nodlopen -o ref_cache/ref-cache ref_cache/cmsg_wrap.o ref_cache/http_parser.o ref_cache/listener.o ref_cache/log_files.o ref_cache/main.o ref_cache/misc.o ref_cache/ping.o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_poll.o ref_cache/ref_files.o ref_cache/request_handler.o ref_cache/sendfile_wrap.o ref_cache/server.o ref_cache/transaction.o ref_cache/upstream.o cram/pooled_alloc.o md5.o -lcurl 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 -fvisibility=hidden -I. -c -o hts.o hts.c ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o plugin.o ranlib libhts.a 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 -fvisibility=hidden -I. -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.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 -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -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 -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico simd.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico plugin.pico -llzma -lbz2 -lz -lm -lpthread ln -sf libhts.so libhts.so.3 lto-wrapper: warning: using serial compilation of 17 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 16 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 16 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -llzma -lbz2 -lz -lm -lpthread 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 -fvisibility=hidden -rdynamic -o test/test_khash test/test_khash.o libhts.a -llzma -lbz2 -lz -lm -lpthread 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 -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -llzma -lbz2 -lz -lm -lpthread 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 -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test_nibbles test/test_nibbles.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 16 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 16 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 17 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 16 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 17 LTRANS jobs gcc -shared -Wl,-E -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 -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -shared -Wl,-E -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 -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -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 -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread 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 -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 17 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs 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 -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 16 LTRANS jobs + sed -i -E '/^(Libs|Requires)\.private:/d' htslib.pc.tmp + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.EKNsjg + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le '!=' / ']' + rm -rf /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le ++ dirname /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le + cd htslib-1.23 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/bin /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/include /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/include/htslib /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/lib64 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/man/man1 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/man/man5 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/man/man7 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/libexec/htslib; fi /usr/bin/install -p -m 644 libhts.so /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/lib64/libhts.so.1.23 ln -sf libhts.so.1.23 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/lib64/libhts.so ln -sf libhts.so.1.23 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/lib64/libhts.so.3 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.23#g' htslib.pc.tmp > /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/lib64/pkgconfig/htslib.pc chmod 644 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/lib64/pkgconfig/htslib.pc /usr/bin/install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so"; then /usr/bin/install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/libexec/htslib; fi /usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/include/htslib /usr/bin/install -p -m 644 libhts.a /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/lib64/libhts.a /usr/bin/install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/man/man1 if test "xref_cache/ref-cache" != "x" ; then \ /usr/bin/install -p -m 644 ref_cache/ref-cache.1 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/man/man1 ; \ fi /usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/man/man5 /usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/man/man7 ~/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/lib64 ~/build/BUILD/htslib-1.23 + pushd /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le//usr/lib64 + chmod 755 libhts.so.1.23 ~/build/BUILD/htslib-1.23 + popd + find /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le -name '*.la' -delete + rm -f /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le//usr/lib64/libhts.a + /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 htslib-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/htslib-1.23 extracting debug info from /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/bin/annot-tsv extracting debug info from /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/bin/htsfile extracting debug info from /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/bin/bgzip extracting debug info from /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/bin/tabix extracting debug info from /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/bin/ref-cache extracting debug info from /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/lib64/libhts.so.1.23 extracting debug info from /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/libexec/htslib/hfile_gcs.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/libexec/htslib/hfile_libcurl.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/libexec/htslib/hfile_s3.so original debug info size: 17024kB, size after compression: 14848kB /usr/bin/sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match. 7140 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.ZBQCTq + umask 022 + cd /builddir/build/BUILD + cd htslib-1.23 + make test sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > htslib-uninstalled.pc 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 -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/rANS_static_test.o htscodecs/tests/rANS_static_test.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 -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x8 htscodecs/tests/rANS_static_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test Testing rans4x8 -r -o0 on ./dat/q4 11674 Testing rans4x8 -r -o1 on ./dat/q4 10870 Testing rans4x8 -r -o0 on ./dat/q40+dir 50258 Testing rans4x8 -r -o1 on ./dat/q40+dir 50537 Testing rans4x8 -r -o0 on ./dat/q8 33099 Testing rans4x8 -r -o1 on ./dat/q8 31428 Testing rans4x8 -r -o0 on ./dat/qvar 32997 Testing rans4x8 -r -o1 on ./dat/qvar 32832 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 -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/rANS_static4x16pr_test.o htscodecs/tests/rANS_static4x16pr_test.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 -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x16pr htscodecs/tests/rANS_static4x16pr_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test Testing rans4x16 -r -o0 on ./dat/q4 11660 Testing rans4x16 -r -o1 on ./dat/q4 10848 Testing rans4x16 -r -o64 on ./dat/q4 12878 Testing rans4x16 -r -o65 on ./dat/q4 10672 Testing rans4x16 -r -o128 on ./dat/q4 10902 Testing rans4x16 -r -o129 on ./dat/q4 10890 Testing rans4x16 -r -o192 on ./dat/q4 11225 Testing rans4x16 -r -o193 on ./dat/q4 10825 Testing rans4x16 -r -o8 on ./dat/q4 11731 Testing rans4x16 -r -o9 on ./dat/q4 11111 Testing rans4x16 -r -o4 on ./dat/q4 11746 11746 11746 11746 Testing rans4x16 -r -o5 on ./dat/q4 10932 10932 10932 10932 Testing rans4x16 -r -o0 on ./dat/q40+dir 50247 Testing rans4x16 -r -o1 on ./dat/q40+dir 49449 Testing rans4x16 -r -o8 on ./dat/q40+dir 50072 Testing rans4x16 -r -o9 on ./dat/q40+dir 50072 Testing rans4x16 -r -o4 on ./dat/q40+dir 50331 50331 50331 50331 Testing rans4x16 -r -o5 on ./dat/q40+dir 49537 49537 49537 49537 Testing rans4x16 -r -o0 on ./dat/q8 33088 Testing rans4x16 -r -o1 on ./dat/q8 31372 Testing rans4x16 -r -o64 on ./dat/q8 33458 Testing rans4x16 -r -o65 on ./dat/q8 31025 Testing rans4x16 -r -o128 on ./dat/q8 32237 Testing rans4x16 -r -o129 on ./dat/q8 31258 Testing rans4x16 -r -o192 on ./dat/q8 32024 Testing rans4x16 -r -o193 on ./dat/q8 31146 Testing rans4x16 -r -o4 on ./dat/q8 33176 33176 33176 33176 Testing rans4x16 -r -o5 on ./dat/q8 31458 31458 31458 31458 Testing rans4x16 -r -o69 on ./dat/qsimd 35 Testing rans4x16 -r -o4 on ./dat/qsimd 219 219 219 219 Testing rans4x16 -r -o5 on ./dat/qsimd 151 151 151 151 Testing rans4x16 -r -o0 on ./dat/qvar 32987 Testing rans4x16 -r -o1 on ./dat/qvar 32261 Testing rans4x16 -r -o4 on ./dat/qvar 33073 33073 33073 33073 Testing rans4x16 -r -o5 on ./dat/qvar 32353 32353 32353 32353 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 -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/arith_dynamic_test.o htscodecs/tests/arith_dynamic_test.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 -fvisibility=hidden -rdynamic -o htscodecs/tests/arith_dynamic htscodecs/tests/arith_dynamic_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./arith.test Testing arith_dynamic -r -o0 on ./dat/q4 11615 Testing arith_dynamic -r -o1 on ./dat/q4 10831 Testing arith_dynamic -r -o64 on ./dat/q4 13360 Testing arith_dynamic -r -o65 on ./dat/q4 10484 Testing arith_dynamic -r -o128 on ./dat/q4 10774 Testing arith_dynamic -r -o129 on ./dat/q4 10329 Testing arith_dynamic -r -o192 on ./dat/q4 11095 Testing arith_dynamic -r -o193 on ./dat/q4 10283 Testing arith_dynamic -r -o8 on ./dat/q4 11448 Testing arith_dynamic -r -o9 on ./dat/q4 11083 Testing arith_dynamic -r -o0 on ./dat/q40+dir 49949 Testing arith_dynamic -r -o1 on ./dat/q40+dir 49034 Testing arith_dynamic -r -o64 on ./dat/q40+dir 51242 Testing arith_dynamic -r -o65 on ./dat/q40+dir 49061 Testing arith_dynamic -r -o8 on ./dat/q40+dir 49820 Testing arith_dynamic -r -o9 on ./dat/q40+dir 49448 Testing arith_dynamic -r -o0 on ./dat/q8 32752 Testing arith_dynamic -r -o1 on ./dat/q8 31331 Testing arith_dynamic -r -o64 on ./dat/q8 35211 Testing arith_dynamic -r -o65 on ./dat/q8 30907 Testing arith_dynamic -r -o128 on ./dat/q8 32063 Testing arith_dynamic -r -o129 on ./dat/q8 31084 Testing arith_dynamic -r -o192 on ./dat/q8 32267 Testing arith_dynamic -r -o193 on ./dat/q8 30931 Testing arith_dynamic -r -o0 on ./dat/qvar 32597 Testing arith_dynamic -r -o1 on ./dat/qvar 31982 Testing arith_dynamic -r -o64 on ./dat/qvar 33237 Testing arith_dynamic -r -o65 on ./dat/qvar 31993 Testing arith_dynamic -r -o1 on ./dat/u32 27005 Testing arith_dynamic -r -o65 on ./dat/u32 23864 Testing arith_dynamic -r -o9 on ./dat/u32 24811 Testing arith_dynamic -r -o4 on ./dat/u32 20849 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 -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/tokenise_name3_test.o htscodecs/tests/tokenise_name3_test.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 -fvisibility=hidden -rdynamic -o htscodecs/tests/tokenise_name3 htscodecs/tests/tokenise_name3_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread lto-wrapper: warning: using serial compilation of 2 LTRANS jobs cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test Testing tokenise_name3 -r -1 on ./names/01.names 2708 Testing tokenise_name3 -r -3 on ./names/01.names 2429 Testing tokenise_name3 -r -5 on ./names/01.names 2264 Testing tokenise_name3 -r -7 on ./names/01.names 2264 Testing tokenise_name3 -r -9 on ./names/01.names 2234 Testing tokenise_name3 -r -11 on ./names/01.names 2449 Testing tokenise_name3 -r -13 on ./names/01.names 2085 Testing tokenise_name3 -r -15 on ./names/01.names 2071 Testing tokenise_name3 -r -17 on ./names/01.names 2070 Testing tokenise_name3 -r -19 on ./names/01.names 2051 Testing tokenise_name3 -r -1 on ./names/02.names 5390 Testing tokenise_name3 -r -3 on ./names/02.names 4955 Testing tokenise_name3 -r -5 on ./names/02.names 4923 Testing tokenise_name3 -r -7 on ./names/02.names 4923 Testing tokenise_name3 -r -9 on ./names/02.names 4918 Testing tokenise_name3 -r -11 on ./names/02.names 4838 Testing tokenise_name3 -r -13 on ./names/02.names 4757 Testing tokenise_name3 -r -15 on ./names/02.names 4743 Testing tokenise_name3 -r -17 on ./names/02.names 4716 Testing tokenise_name3 -r -19 on ./names/02.names 4700 Testing tokenise_name3 -r -1 on ./names/03.names 8854 Testing tokenise_name3 -r -3 on ./names/03.names 7782 Testing tokenise_name3 -r -5 on ./names/03.names 7771 Testing tokenise_name3 -r -7 on ./names/03.names 7771 Testing tokenise_name3 -r -9 on ./names/03.names 7521 Testing tokenise_name3 -r -11 on ./names/03.names 7395 Testing tokenise_name3 -r -13 on ./names/03.names 7252 Testing tokenise_name3 -r -15 on ./names/03.names 7252 Testing tokenise_name3 -r -17 on ./names/03.names 7225 Testing tokenise_name3 -r -19 on ./names/03.names 7075 Testing tokenise_name3 -r -1 on ./names/05.names 3787 Testing tokenise_name3 -r -3 on ./names/05.names 3564 Testing tokenise_name3 -r -5 on ./names/05.names 3536 Testing tokenise_name3 -r -7 on ./names/05.names 3536 Testing tokenise_name3 -r -9 on ./names/05.names 3534 Testing tokenise_name3 -r -11 on ./names/05.names 3411 Testing tokenise_name3 -r -13 on ./names/05.names 3397 Testing tokenise_name3 -r -15 on ./names/05.names 3383 Testing tokenise_name3 -r -17 on ./names/05.names 3383 Testing tokenise_name3 -r -19 on ./names/05.names 3377 Testing tokenise_name3 -r -1 on ./names/08.names 5579 Testing tokenise_name3 -r -3 on ./names/08.names 5274 Testing tokenise_name3 -r -5 on ./names/08.names 5246 Testing tokenise_name3 -r -7 on ./names/08.names 5213 Testing tokenise_name3 -r -9 on ./names/08.names 5160 Testing tokenise_name3 -r -11 on ./names/08.names 4915 Testing tokenise_name3 -r -13 on ./names/08.names 4901 Testing tokenise_name3 -r -15 on ./names/08.names 4887 Testing tokenise_name3 -r -17 on ./names/08.names 4844 Testing tokenise_name3 -r -19 on ./names/08.names 4805 Testing tokenise_name3 -r -1 on ./names/09.names 3740 Testing tokenise_name3 -r -3 on ./names/09.names 3539 Testing tokenise_name3 -r -5 on ./names/09.names 3539 Testing tokenise_name3 -r -7 on ./names/09.names 3528 Testing tokenise_name3 -r -9 on ./names/09.names 3493 Testing tokenise_name3 -r -11 on ./names/09.names 3431 Testing tokenise_name3 -r -13 on ./names/09.names 3394 Testing tokenise_name3 -r -15 on ./names/09.names 3394 Testing tokenise_name3 -r -17 on ./names/09.names 3386 Testing tokenise_name3 -r -19 on ./names/09.names 3366 Testing tokenise_name3 -r -1 on ./names/10.names 5210 Testing tokenise_name3 -r -3 on ./names/10.names 4782 Testing tokenise_name3 -r -5 on ./names/10.names 4752 Testing tokenise_name3 -r -7 on ./names/10.names 4752 Testing tokenise_name3 -r -9 on ./names/10.names 4744 Testing tokenise_name3 -r -11 on ./names/10.names 4566 Testing tokenise_name3 -r -13 on ./names/10.names 4520 Testing tokenise_name3 -r -15 on ./names/10.names 4506 Testing tokenise_name3 -r -17 on ./names/10.names 4494 Testing tokenise_name3 -r -19 on ./names/10.names 4476 Testing tokenise_name3 -r -1 on ./names/20.names 1783 Testing tokenise_name3 -r -3 on ./names/20.names 1668 Testing tokenise_name3 -r -5 on ./names/20.names 1640 Testing tokenise_name3 -r -7 on ./names/20.names 1640 Testing tokenise_name3 -r -9 on ./names/20.names 1632 Testing tokenise_name3 -r -11 on ./names/20.names 1645 Testing tokenise_name3 -r -13 on ./names/20.names 1625 Testing tokenise_name3 -r -15 on ./names/20.names 1611 Testing tokenise_name3 -r -17 on ./names/20.names 1609 Testing tokenise_name3 -r -19 on ./names/20.names 1600 Testing tokenise_name3 -r -1 on ./names/nv.names 5273 Testing tokenise_name3 -r -3 on ./names/nv.names 4968 Testing tokenise_name3 -r -5 on ./names/nv.names 4941 Testing tokenise_name3 -r -7 on ./names/nv.names 4941 Testing tokenise_name3 -r -9 on ./names/nv.names 4937 Testing tokenise_name3 -r -11 on ./names/nv.names 4864 Testing tokenise_name3 -r -13 on ./names/nv.names 4785 Testing tokenise_name3 -r -15 on ./names/nv.names 4772 Testing tokenise_name3 -r -17 on ./names/nv.names 4772 Testing tokenise_name3 -r -19 on ./names/nv.names 4767 Testing tokenise_name3 -r -1 on ./names/nv2.names 1060 Testing tokenise_name3 -r -3 on ./names/nv2.names 891 Testing tokenise_name3 -r -5 on ./names/nv2.names 863 Testing tokenise_name3 -r -7 on ./names/nv2.names 863 Testing tokenise_name3 -r -9 on ./names/nv2.names 855 Testing tokenise_name3 -r -11 on ./names/nv2.names 836 Testing tokenise_name3 -r -13 on ./names/nv2.names 799 Testing tokenise_name3 -r -15 on ./names/nv2.names 785 Testing tokenise_name3 -r -17 on ./names/nv2.names 779 Testing tokenise_name3 -r -19 on ./names/nv2.names 767 Testing tokenise_name3 -r -1 on ./names/rr.names 6605 Testing tokenise_name3 -r -3 on ./names/rr.names 6237 Testing tokenise_name3 -r -5 on ./names/rr.names 6237 Testing tokenise_name3 -r -7 on ./names/rr.names 6237 Testing tokenise_name3 -r -9 on ./names/rr.names 6230 Testing tokenise_name3 -r -11 on ./names/rr.names 6151 Testing tokenise_name3 -r -13 on ./names/rr.names 6025 Testing tokenise_name3 -r -15 on ./names/rr.names 6025 Testing tokenise_name3 -r -17 on ./names/rr.names 6023 Testing tokenise_name3 -r -19 on ./names/rr.names 5973 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 -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/fqzcomp_qual_test.o htscodecs/tests/fqzcomp_qual_test.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 -fvisibility=hidden -rdynamic -o htscodecs/tests/fqzcomp_qual htscodecs/tests/fqzcomp_qual_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./fqzcomp.test 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 -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/varint_test.o htscodecs/tests/varint_test.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 -fvisibility=hidden -rdynamic -o htscodecs/tests/varint htscodecs/tests/varint_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && ./varint test/hts_endian test/test_expr test/test_kfunc test/test_khash test/test_kstring test/test_nibbles -v test/test_str2int test/test_time_funcs test/fieldarith test/fieldarith.sam test/hfile if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ fi if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ fi test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/faidx && ./test-faidx.sh faidx.tst Testing faidx... PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225 Expected passes: 25 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/sam_filter && ./filter.sh filter.tst Testing sam_filter... PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' Expected passes: 18 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz -@ 2 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2 Expected passes: 16 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam PASS : $pileup -m mp_overlap1.sam PASS : $pileup -m mp_overlap2.sam Expected passes: 23 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/fastq && ./test-fastq.sh Testing fastq support PASS : $tview minimal.fq PASS : $tview minimal.fa PASS : $tview multiline.fq PASS : $tview multiline.fa PASS : $tview -i fastq_aux longline.fq PASS : $tview single.fq PASS : $tview single.fa PASS : $tview -i fastq_aux single.fq PASS : $tview -i fastq_aux single.fa PASS : $tview interleaved.fq PASS : $tview interleaved.fa PASS : $tview -i fastq_aux interleaved.fq PASS : $tview -i fastq_aux interleaved.fa PASS : $tview -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_casava filter_casava.fq PASS : $tview -i fastq_casava filter_casava.fa PASS : $tview -i fastq_aux r1.fq PASS : $tview -i fastq_aux r2.fq PASS : $tview -i fastq_aux r1.fa PASS : $tview -i fastq_aux r2.fa PASS : $tview -i fastq_name2 name2.fq PASS : $tview -i fastq_name2 name2.fa PASS : $tview -i fastq_umi=RX UMI.fq PASS : $tview -f minimal.sam PASS : $tview -F minimal.sam PASS : $tview -f -o fastq_aux single_aux.sam PASS : $tview -F -o fastq_aux single_aux.sam PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -f -o fastq_casava inter_casava.sam PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -F -o fastq_casava inter_casava.sam PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -f -o fastq_casava filter_casava.sam PASS : $tview -F -o fastq_casava filter_casava.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -f -o fastq_rnum -o fastq_umi UMI.sam Expected passes: 43 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/base_mods && ./base-mods.sh base-mods.tst Testing base-modifications... PASS : $test_mod MM-chebi.sam PASS : $test_mod MM-double.sam PASS : $test_mod MM-multi.sam PASS : $test_mod MM-explicit.sam PASS : $test_mod -x MM-explicit.sam PASS : $test_mod -f 1 MM-explicit.sam PASS : $test_mod MM-not-all-modded.sam PASS : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam PASS : $pileup_mod < MM-MNp.sam PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-MNf1.sam (must exit non-zero) PASS : $test_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-bounds+.sam (must exit non-zero) PASS : $test_mod < MM-bounds-.sam (must exit non-zero) PASS : $test_mod -f 1 MM-variants.sam Expected passes: 17 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tlen && ./tlen.sh tlen.tst Testing CRAM TLEN auto-creation... PASS : $test_view a7.cram PASS : $test_view a7b.cram PASS : $test_view a8.cram PASS : $test_view a8b.cram PASS : $test_view a9.cram PASS : $test_view a9b.cram PASS : $test_view b7.cram PASS : $test_view b7b.cram PASS : $test_view b8.cram PASS : $test_view b8b.cram PASS : $test_view c7.cram PASS : $test_view c7b.cram PASS : $test_view c8.cram PASS : $test_view c8b.cram PASS : $test_view d7.cram PASS : $test_view d7b.cram PASS : $test_view d4.cram PASS : $test_view d4b.cram PASS : $test_view d4c.cram PASS : $test_view d4d.cram PASS : $test_view d4e.cram PASS : $test_view d4f.cram PASS : $test_view d5.cram PASS : $test_view d5b.cram PASS : $test_view d5c.cram PASS : $test_view d5d.cram PASS : $test_view d5e.cram PASS : $test_view d5f.cram PASS : $test_view a4.cram PASS : $test_view a5.cram Expected passes: 30 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq (Expect trailing 'x' message for " -1,001x") [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] (Expect trailing 'k' message for "1.5e+3k") [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] (Expect dropped fraction message for "12.3456k") [W::hts_parse_decimal] Discarding fractional part of 12.3456k [W::hts_parse_decimal] Discarding fractional part of 12.3456k (Expect invalid numeric message for "A") [W::hts_parse_decimal] Invalid numeric value A[truncated] (Expect invalid numeric message for "G") [W::hts_parse_decimal] Invalid numeric value G[truncated] (Expect invalid numeric message for " +/-") [W::hts_parse_decimal] Invalid numeric value +/-[truncated] (Expect invalid numeric message for " -.e+9999") [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] test/test-regidx cd test && \ if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \ REF_PATH=: HTS_PATH=.. ./with-shlib.sh ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \ else \ REF_PATH=: ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \ fi bgzip round-trip no threads: .. ok bgzip text mode round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip multifile no threads: .. ok bgzip --output no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip text mode round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok bgzip multifile 4 threads: .. ok bgzip --output 4 threads: .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -b -m 14 -x /tmp/7cjcVO_y8I/index.bam.csi /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/7cjcVO_y8I/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/7cjcVO_y8I/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -b -m 0 -x /tmp/7cjcVO_y8I/index.bam.bai /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/7cjcVO_y8I/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -b /tmp/7cjcVO_y8I/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -z -m 14 -x /tmp/7cjcVO_y8I/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -z -m 0 -x /tmp/7cjcVO_y8I/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -b /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -z -m 14 -x /tmp/7cjcVO_y8I/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23/test/index_dos.sam > /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -z -m 0 -x /tmp/7cjcVO_y8I/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23/test/index_dos.sam > /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -b /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -C -x /tmp/7cjcVO_y8I/index.cram.crai /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/7cjcVO_y8I/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index /tmp/7cjcVO_y8I/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -p /tmp/7cjcVO_y8I/index3_rgn.sam /tmp/7cjcVO_y8I/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -M -p /tmp/7cjcVO_y8I/index3_rgnm.sam /tmp/7cjcVO_y8I/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -b -m 14 -x /tmp/7cjcVO_y8I/index.bcf.csi /builddir/build/BUILD/htslib-1.23/test/index.vcf > /tmp/7cjcVO_y8I/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/7cjcVO_y8I/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -z -m 14 -x /tmp/7cjcVO_y8I/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.23/test/index.vcf > /tmp/7cjcVO_y8I/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/7cjcVO_y8I/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -z -m 0 -x /tmp/7cjcVO_y8I/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.23/test/index.vcf > /tmp/7cjcVO_y8I/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -t /tmp/7cjcVO_y8I/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/tabix /tmp/7cjcVO_y8I/index.vcf.gz##idx##/tmp/7cjcVO_y8I/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/7cjcVO_y8I/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/7cjcVO_y8I/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/7cjcVO_y8I/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/7cjcVO_y8I/index2.bam 2:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -b -m 14 -x /tmp/7cjcVO_y8I/index.bam.csi /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/7cjcVO_y8I/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/7cjcVO_y8I/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -b -m 0 -x /tmp/7cjcVO_y8I/index.bam.bai /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/7cjcVO_y8I/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -b /tmp/7cjcVO_y8I/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -z -m 14 -x /tmp/7cjcVO_y8I/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -z -m 0 -x /tmp/7cjcVO_y8I/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -b /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -z -m 14 -x /tmp/7cjcVO_y8I/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23/test/index_dos.sam > /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -z -m 0 -x /tmp/7cjcVO_y8I/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23/test/index_dos.sam > /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -b /tmp/7cjcVO_y8I/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -C -x /tmp/7cjcVO_y8I/index.cram.crai /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/7cjcVO_y8I/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index /tmp/7cjcVO_y8I/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -p /tmp/7cjcVO_y8I/index3_rgn.sam /tmp/7cjcVO_y8I/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -M -p /tmp/7cjcVO_y8I/index3_rgnm.sam /tmp/7cjcVO_y8I/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -b -m 14 -x /tmp/7cjcVO_y8I/index.bcf.csi /builddir/build/BUILD/htslib-1.23/test/index.vcf > /tmp/7cjcVO_y8I/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/7cjcVO_y8I/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -z -m 14 -x /tmp/7cjcVO_y8I/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.23/test/index.vcf > /tmp/7cjcVO_y8I/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/7cjcVO_y8I/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -z -m 0 -x /tmp/7cjcVO_y8I/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.23/test/index.vcf > /tmp/7cjcVO_y8I/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -t /tmp/7cjcVO_y8I/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/tabix /tmp/7cjcVO_y8I/index.vcf.gz##idx##/tmp/7cjcVO_y8I/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/7cjcVO_y8I/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/7cjcVO_y8I/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/7cjcVO_y8I/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/7cjcVO_y8I/index2.bam 2:2000000-2000000 .. ok test_view testing multi-ref CRAM modes: ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing multi-ref CRAM modes: ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated2.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated2.sam > xx#repeated2.tmp.bam ./test_view xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.sam_ ./compare_sam.pl xx#repeated2.sam xx#repeated2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated2.sam > xx#repeated2.tmp.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view -D xx#repeated2.tmp.cram > xx#repeated2.tmp.cram.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view xx#repeated2.tmp.bam.cram > xx#repeated2.tmp.bam.cram.bam.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#u.sam, ref xx.fa: ./test_view -S -l0 -b xx#u.sam > xx#u.tmp.bam ./test_view xx#u.tmp.bam > xx#u.tmp.bam.sam_ ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram ./test_view -D xx#u.tmp.cram > xx#u.tmp.cram.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram ./test_view xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference "CHROMOSOME_I" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam ./test_view -C -p c1#bounds_er.tmp.cram c1#bounds.sam [W::cram_get_ref] Failed to populate reference "c1" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam ./test_view -o embed_ref=2 -o seqs_per_slice=3 -o bases_per_slice=1000000 -C -p embed_MD.tmp.cram embed_MD.sam ./test_view -p embed_MD.tmp.cram.sam embed_MD.tmp.cram ./compare_sam.pl embed_MD.sam embed_MD.tmp.cram.sam .. ok test_view testing region queries: ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /builddir/build/BUILD/htslib-1.23/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#bounds_er.tmp.cram.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.bam ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.cram ./test_view -@4 -D c1#bounds_er.tmp.cram.tmp.cram > c1#bounds_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.cram ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam.cram > c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated2.sam > xx#repeated2.tmp.bam ./test_view -@4 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.sam_ ./compare_sam.pl xx#repeated2.sam xx#repeated2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated2.sam > xx#repeated2.tmp.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view -@4 -D xx#repeated2.tmp.cram > xx#repeated2.tmp.cram.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view -@4 xx#repeated2.tmp.bam.cram > xx#repeated2.tmp.bam.cram.bam.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ .. ok test_view testing xx#u.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#u.sam > xx#u.tmp.bam ./test_view -@4 xx#u.tmp.bam > xx#u.tmp.bam.sam_ ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram ./test_view -@4 -D xx#u.tmp.cram > xx#u.tmp.cram.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram ./test_view -@4 xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -@4 -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -@4 -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference "CHROMOSOME_I" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam ./test_view -@4 -C -p c1#bounds_er.tmp.cram c1#bounds.sam [W::cram_get_ref] Failed to populate reference "c1" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam ./test_view -@4 -o embed_ref=2 -o seqs_per_slice=3 -o bases_per_slice=1000000 -C -p embed_MD.tmp.cram embed_MD.sam ./test_view -@4 -p embed_MD.tmp.cram.sam embed_MD.tmp.cram ./compare_sam.pl embed_MD.sam embed_MD.tmp.cram.sam .. ok test_view testing region queries: ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -@4 -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /builddir/build/BUILD/htslib-1.23/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_MD testing xx#MD.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ Checking for MD/NM in xx#MD.sam ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_MD testing xx#MD2.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_vcf_api: /builddir/build/BUILD/htslib-1.23/test/test-vcf-api /tmp/7cjcVO_y8I/test-vcf-api.bcf .. ok test_bcf2vcf: /builddir/build/BUILD/htslib-1.23/test/test_view /builddir/build/BUILD/htslib-1.23/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /builddir/build/BUILD/htslib-1.23/test/test-vcf-sweep /tmp/7cjcVO_y8I/test-vcf-api.bcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23/htsfile -ch /builddir/build/BUILD/htslib-1.23/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23/test/formatcols.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23/test/noroundtrip.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23/test/formatmissing.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23/test/vcf_meta_meta.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23/test/test_view /builddir/build/BUILD/htslib-1.23/test/modhdr.vcf.gz chr22:1-2 .. ok test_vcf_44: /builddir/build/BUILD/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23/test/vcf44_1.vcf .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/7cjcVO_y8I -s 74452500 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/7cjcVO_y8I -s 34270147 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/7cjcVO_y8I -s 11108528 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/7cjcVO_y8I -s 42233895 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/7cjcVO_y8I -s 8111117 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/7cjcVO_y8I -s 85644070 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/7cjcVO_y8I -s 49879942 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/7cjcVO_y8I -s 47881429 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/7cjcVO_y8I -s 69081244 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/7cjcVO_y8I -s 83459376 .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.b.vcf /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/7cjcVO_y8I/no_index_1.err .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/7cjcVO_y8I/no_index_2.out 2> /tmp/7cjcVO_y8I/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/7cjcVO_y8I/no_index_3.out 2> /tmp/7cjcVO_y8I/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.rec_order.vcf /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf > /tmp/7cjcVO_y8I/no_index_4.out 2> /tmp/7cjcVO_y8I/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test_view -b -p /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf -x /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf.csi /builddir/build/BUILD/htslib-1.23/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_1.out.vcf -r '1' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_2.out.vcf -r '1:1-2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_4.out.vcf -r '1:1-1' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_5.out.vcf -r '{1:1}' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set regions .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_14.out.vcf -t '1' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_15.out.vcf -t '1:1-2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_17.out.vcf -t '1:1-1' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_18.out.vcf -t '{1:1}' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/7cjcVO_y8I/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/7cjcVO_y8I/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set targets .. ok .. ok test_command: /builddir/build/BUILD/htslib-1.23/test/test-bcf-translate - .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.23/test/test_view -t ce.fa -C /tmp/7cjcVO_y8I/headernul0.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.23/test/test_view -t ce.fa -C /tmp/7cjcVO_y8I/headernul1.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.23/test/test_view -t ce.fa -C /tmp/7cjcVO_y8I/headernul678.bam .. ok test_rebgzip: /builddir/build/BUILD/htslib-1.23/bgzip -I /builddir/build/BUILD/htslib-1.23/test/bgziptest.txt.gz.gzi -c -g /builddir/build/BUILD/htslib-1.23/test/bgziptest.txt .. ok test-logging: /builddir/build/BUILD/htslib-1.23/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/builddir/build/BUILD/htslib-1.23 /builddir/build/BUILD/htslib-1.23/test/with-shlib.sh /builddir/build/BUILD/htslib-1.23/htsfile https://localhost:99999/invalid_port .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23/test/realn01.fa -i /builddir/build/BUILD/htslib-1.23/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -a -f /builddir/build/BUILD/htslib-1.23/test/realn01.fa -i /builddir/build/BUILD/htslib-1.23/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -a -f /builddir/build/BUILD/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -e -f /builddir/build/BUILD/htslib-1.23/test/realn01.fa -i /builddir/build/BUILD/htslib-1.23/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -e -f /builddir/build/BUILD/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -r -f /builddir/build/BUILD/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23/test/realn02-r.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -a -f /builddir/build/BUILD/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23/test/realn02_exp.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23/test/realn02_exp-a.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23/test/realn03.fa -e -i /builddir/build/BUILD/htslib-1.23/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /builddir/build/BUILD/htslib-1.23/test/test-bcf_set_variant_type .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -c chr,beg,end -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -c chr,beg,end -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -c chr,beg,end -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl,value:overlap,value -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl,value:overlap,value -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl,value:overlap,value -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -O 0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -O 0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -O 0.5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -rO 0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -rO 0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -rO 0.5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.3.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.3.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.3.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -a nbp,frac -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.4.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.4.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.4.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.5.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.5.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.5.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.6.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.6.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.6.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.7.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.7.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.7.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.8.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.8.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.8.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.9.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.9.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.9.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -x -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -x -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -x -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -f smpl -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -f smpl -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -f smpl -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -x -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -x -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -x -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.12.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.12.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.12.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.12.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.12.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -C 11:11 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.14.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.14.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -C 11:11 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.14.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -C 11:11 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -C 01:01 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.14.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.14.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -C 01:01 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.14.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -C 01:01 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.14.txt .. ok ref-cache: ./test_view -C -p ref_cache/ce_m5.sam.tmp.cram ref_cache/ce_m5.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.2.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.2.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.3.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.3.sam .. ok Number of tests: total .. 358 passed .. 358 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: htslib-1.23-1.el9.ppc64le Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.CIgEBQ + umask 022 + cd /builddir/build/BUILD + cd htslib-1.23 + DOCDIR=/builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/doc/htslib + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/doc/htslib + cp -pr NEWS /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/doc/htslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.CP6qTK + umask 022 + cd /builddir/build/BUILD + cd htslib-1.23 + LICENSEDIR=/builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/licenses/htslib + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/licenses/htslib + cp -pr LICENSE /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le/usr/share/licenses/htslib + RPM_EC=0 ++ jobs -p + exit 0 Provides: htslib = 1.23-1.el9 htslib(ppc-64) = 1.23-1.el9 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_1.13)(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_1.20)(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) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libbz2.so.1()(64bit) 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) libcrypto.so.3()(64bit) libcrypto.so.3(OPENSSL_3.0.0)(64bit) libcurl.so.4()(64bit) libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(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_1.7)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-devel-1.23-1.el9.ppc64le Provides: htslib-devel = 1.23-1.el9 htslib-devel(ppc-64) = 1.23-1.el9 pkgconfig(htslib) = 1.23 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/pkg-config libhts.so.3()(64bit) Processing files: htslib-tools-1.23-1.el9.ppc64le Provides: htslib-tools = 1.23-1.el9 htslib-tools(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: libbz2.so.1()(64bit) 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) libcurl.so.4()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-debugsource-1.23-1.el9.ppc64le Provides: htslib-debugsource = 1.23-1.el9 htslib-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: htslib-debuginfo-1.23-1.el9.ppc64le Provides: debuginfo(build-id) = 05907a893fa1041d4675a37aa727bf95ba942c42 debuginfo(build-id) = 32c791f190d40cbaa6168ba6ee28b7799aaa6827 debuginfo(build-id) = 4b16d4a56d0a82ac7ba23ec635b17b063cb46b6c debuginfo(build-id) = 5ae1fbd6977e82176a702d31c1c5b7cb7fd596cc htslib-debuginfo = 1.23-1.el9 htslib-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: htslib-debugsource(ppc-64) = 1.23-1.el9 Processing files: htslib-tools-debuginfo-1.23-1.el9.ppc64le Provides: debuginfo(build-id) = 0239c4f9b6a06ba3ee77944c45683dc080c23dcd debuginfo(build-id) = 1dc20f1e14221d66ea0b48f6694266fc553b50c0 debuginfo(build-id) = 6ad6c3bfecd4f323d2d2f4a436b31e10ac45615f debuginfo(build-id) = cc443b8b63a53f8eda7bfe18a936582a5aa86b4e debuginfo(build-id) = ebb6f098418e546313ab3878f5ef5eb5f40cbbc4 htslib-tools-debuginfo = 1.23-1.el9 htslib-tools-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: htslib-debugsource(ppc-64) = 1.23-1.el9 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le Wrote: /builddir/build/RPMS/htslib-1.23-1.el9.ppc64le.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.23-1.el9.ppc64le.rpm Wrote: /builddir/build/RPMS/htslib-debuginfo-1.23-1.el9.ppc64le.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.23-1.el9.ppc64le.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.23-1.el9.ppc64le.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.23-1.el9.ppc64le.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.qQ4Uo0 + umask 022 + cd /builddir/build/BUILD + cd htslib-1.23 + /usr/bin/rm -rf /builddir/build/BUILDROOT/htslib-1.23-1.el9.ppc64le + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild htslib-1.23-1.el9.src.rpm Finish: build phase for htslib-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-1769500626.765335/root/var/log/dnf.rpm.log /var/lib/mock/rhel+epel-9-ppc64le-1769500626.765335/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-9-ppc64le-1769500626.765335/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/htslib-1.23-1.el9.src.rpm) Config(child) 6 minutes 5 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": "htslib-tools-debuginfo", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "ppc64le" }, { "name": "htslib-tools", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "ppc64le" }, { "name": "htslib-devel", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "ppc64le" }, { "name": "htslib-debugsource", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "ppc64le" }, { "name": "htslib", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "ppc64le" }, { "name": "htslib", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "src" }, { "name": "htslib-debuginfo", "epoch": null, "version": "1.23", "release": "1.el9", "arch": "ppc64le" } ] } RPMResults finished