Warning: Permanently added '162.133.130.70' (ED25519) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 4733910 --chroot fedora-rawhide-s390x --detached Version: 0.61 PID: 5406 Logging PID: 5407 Task: {'appstream': True, 'background': False, 'bootstrap': 'off', 'build_id': 4733910, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-s390x', 'enable_net': False, 'fedora_review': False, 'git_hash': '00e9239ef0d1f3ea39c07da84538bfbc7d86f9dd', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jaruga/staging/samtools', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'samtools', 'package_version': '1.15.1-1.fc38', 'project_dirname': 'staging', 'project_name': 'staging', 'project_owner': 'jaruga', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jaruga/staging/fedora-rawhide-s390x/', 'id': 'copr_base', 'name': 'Copr repository'}], 'sandbox': 'jaruga/staging--jaruga', 'source_json': {}, 'source_type': None, 'submitter': 'jaruga', 'tags': [], 'task_id': '4733910-fedora-rawhide-s390x', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jaruga/staging/samtools /var/lib/copr-rpmbuild/workspace/workdir-rabtnn8f/samtools --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jaruga/staging/samtools', '/var/lib/copr-rpmbuild/workspace/workdir-rabtnn8f/samtools', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-rabtnn8f/samtools'... Running: git checkout 00e9239ef0d1f3ea39c07da84538bfbc7d86f9dd cmd: ['git', 'checkout', '00e9239ef0d1f3ea39c07da84538bfbc7d86f9dd'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-rabtnn8f/samtools rc: 0 stdout: stderr: Note: switching to '00e9239ef0d1f3ea39c07da84538bfbc7d86f9dd'. 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 00e9239 automatic import of samtools Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-rabtnn8f/samtools rc: 0 stdout: /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading samtools-1.15.1.tar.bz2 INFO: Calling: curl -H Pragma: -o samtools-1.15.1.tar.bz2 --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jaruga/staging/samtools/samtools-1.15.1.tar.bz2/md5/b71d1aa1de9749773b1a04bf54281ca0/samtools-1.15.1.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 7648k 100 7648k 0 0 1022k 0 0:00:07 0:00:07 --:--:-- 1600k INFO: Reading stdout from command: md5sum samtools-1.15.1.tar.bz2 Running (timeout=18000): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-rabtnn8f/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-rabtnn8f/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1660573664.597255 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.1 starting (python version = 3.10.4, NVR = mock-3.1-1.fc35)... 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-rabtnn8f/samtools/samtools.spec) Config(fedora-rawhide-s390x) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1660573664.597255/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 Mock Version: 3.1 INFO: Mock Version: 3.1 Start: dnf install 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 1.3 kB/s | 16 kB 00:11 fedora 3.0 MB/s | 59 MB 00:19 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash s390x 5.1.16-3.fc37 fedora 1.7 M bzip2 s390x 1.0.8-12.fc37 fedora 51 k coreutils s390x 9.1-6.fc37 fedora 1.1 M cpio s390x 2.13-13.fc37 fedora 272 k diffutils s390x 3.8-3.fc37 fedora 377 k fedora-release-common noarch 38-0.2 fedora 22 k findutils s390x 1:4.9.0-2.fc37 fedora 487 k gawk s390x 5.1.1-4.fc37 fedora 1.0 M glibc-minimal-langpack s390x 2.36-1.fc37 fedora 81 k grep s390x 3.7-4.fc37 fedora 272 k gzip s390x 1.12-2.fc37 fedora 166 k info s390x 6.8-4.fc37 fedora 220 k patch s390x 2.7.6-17.fc37 fedora 122 k redhat-rpm-config noarch 227-1.fc37 fedora 80 k rpm-build s390x 4.18.0-0.beta1.4.fc37 fedora 75 k sed s390x 4.8-11.fc37 fedora 304 k shadow-utils s390x 2:4.11.1-4.fc37 fedora 1.1 M tar s390x 2:1.34-3.fc36 fedora 874 k unzip s390x 6.0-58.fc37 fedora 174 k util-linux s390x 2.38.1-1.fc37 fedora 2.3 M which s390x 2.21-35.fc37 fedora 41 k xz s390x 5.2.5-10.fc37 fedora 222 k Installing dependencies: alternatives s390x 1.19-3.fc37 fedora 35 k ansible-srpm-macros noarch 1-6.fc37 fedora 7.5 k audit-libs s390x 3.0.8-3.fc37 fedora 113 k authselect s390x 1.4.0-3.fc37 fedora 144 k authselect-libs s390x 1.4.0-3.fc37 fedora 245 k basesystem noarch 11-14.fc37 fedora 7.0 k binutils s390x 2.38-24.fc38 fedora 9.3 M binutils-gold s390x 2.38-24.fc38 fedora 1.4 M bzip2-libs s390x 1.0.8-12.fc37 fedora 42 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils-common s390x 9.1-6.fc37 fedora 2.0 M cracklib s390x 2.9.6-28.fc36 fedora 91 k crypto-policies noarch 20220802-1.gita99dfd2.fc37 fedora 86 k curl s390x 7.84.0-2.fc37 fedora 310 k cyrus-sasl-lib s390x 2.1.28-7.fc37 fedora 757 k debugedit s390x 5.0-5.fc37 fedora 76 k dwz s390x 0.14-7.fc37 fedora 126 k ed s390x 1.18-2.fc37 fedora 78 k efi-srpm-macros noarch 5-6.fc37 fedora 22 k elfutils s390x 0.187-6.fc37 fedora 518 k elfutils-debuginfod-client s390x 0.187-6.fc37 fedora 39 k elfutils-default-yama-scope noarch 0.187-6.fc37 fedora 17 k elfutils-libelf s390x 0.187-6.fc37 fedora 197 k elfutils-libs s390x 0.187-6.fc37 fedora 253 k fedora-gpg-keys noarch 38-0.2 fedora 125 k fedora-release noarch 38-0.2 fedora 12 k fedora-release-identity-basic noarch 38-0.2 fedora 12 k fedora-repos noarch 38-0.2 fedora 10 k fedora-repos-rawhide noarch 38-0.2 fedora 9.6 k file s390x 5.42-4.fc37 fedora 48 k file-libs s390x 5.42-4.fc37 fedora 675 k filesystem s390x 3.18-2.fc37 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-8.fc37 fedora 26 k fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k gdb-minimal s390x 12.1-4.fc37 fedora 3.5 M gdbm-libs s390x 1:1.23-2.fc37 fedora 56 k ghc-srpm-macros noarch 1.5.0-7.fc37 fedora 7.8 k glibc s390x 2.36-1.fc37 fedora 1.7 M glibc-common s390x 2.36-1.fc37 fedora 352 k glibc-gconv-extra s390x 2.36-1.fc37 fedora 1.6 M gmp s390x 1:6.2.1-3.fc37 fedora 284 k gnat-srpm-macros noarch 4-16.fc37 fedora 8.3 k go-srpm-macros noarch 3.1.0-4.fc37 fedora 27 k jansson s390x 2.13.1-5.fc37 fedora 42 k kernel-srpm-macros noarch 1.0-15.fc37 fedora 9.4 k keyutils-libs s390x 1.6.1-5.fc37 fedora 31 k krb5-libs s390x 1.19.2-11.fc37.1 fedora 706 k libacl s390x 2.3.1-4.fc37 fedora 23 k libarchive s390x 3.6.1-2.fc37 fedora 388 k libattr s390x 2.5.1-5.fc37 fedora 18 k libblkid s390x 2.38.1-1.fc37 fedora 102 k libbrotli s390x 1.0.9-9.fc37 fedora 317 k libcap s390x 2.48-5.fc37 fedora 66 k libcap-ng s390x 0.8.3-3.fc37 fedora 32 k libcom_err s390x 1.46.5-3.fc37 fedora 25 k libcurl s390x 7.84.0-2.fc37 fedora 298 k libdb s390x 5.3.28-53.fc37 fedora 720 k libeconf s390x 0.4.0-4.fc37 fedora 26 k libevent s390x 2.1.12-7.fc37 fedora 252 k libfdisk s390x 2.38.1-1.fc37 fedora 154 k libffi s390x 3.4.2-9.fc37 fedora 34 k libgcc s390x 12.1.1-4.fc38 fedora 79 k libgomp s390x 12.1.1-4.fc38 fedora 290 k libidn2 s390x 2.3.3-2.fc37 fedora 113 k libmount s390x 2.38.1-1.fc37 fedora 131 k libnghttp2 s390x 1.48.0-2.fc37 fedora 72 k libnsl2 s390x 2.0.0-4.fc37 fedora 30 k libpkgconf s390x 1.8.0-3.fc37 fedora 34 k libpsl s390x 0.21.1-6.fc37 fedora 63 k libpwquality s390x 1.4.4-11.fc37 fedora 116 k libselinux s390x 3.4-5.fc37 fedora 83 k libsemanage s390x 3.4-5.fc37 fedora 114 k libsepol s390x 3.4-3.fc37 fedora 298 k libsigsegv s390x 2.14-3.fc37 fedora 27 k libsmartcols s390x 2.38.1-1.fc37 fedora 63 k libssh s390x 0.9.6-5.fc37 fedora 190 k libssh-config noarch 0.9.6-5.fc37 fedora 7.8 k libstdc++ s390x 12.1.1-4.fc38 fedora 836 k libtasn1 s390x 4.18.0-3.fc37 fedora 72 k libtirpc s390x 1.3.3-0.fc37 fedora 90 k libunistring s390x 1.0-2.fc37 fedora 547 k libutempter s390x 1.2.1-7.fc37 fedora 26 k libuuid s390x 2.38.1-1.fc37 fedora 27 k libverto s390x 0.3.2-4.fc37 fedora 20 k libxcrypt s390x 4.4.28-3.fc38 fedora 119 k libxml2 s390x 2.9.14-3.fc37 fedora 712 k libzstd s390x 1.5.2-3.fc37 fedora 274 k lua-libs s390x 5.4.4-4.fc37 fedora 211 k lua-srpm-macros noarch 1-7.fc37 fedora 8.8 k lz4-libs s390x 1.9.3-5.fc37 fedora 68 k mpfr s390x 4.1.0-10.fc37 fedora 254 k ncurses-base noarch 6.3-3.20220501.fc37 fedora 86 k ncurses-libs s390x 6.3-3.20220501.fc37 fedora 319 k nim-srpm-macros noarch 3-7.fc37 fedora 8.4 k ocaml-srpm-macros noarch 7-2.fc37 fedora 13 k openblas-srpm-macros noarch 2-12.fc37 fedora 7.5 k openldap s390x 2.6.2-5.fc38 fedora 248 k openssl-libs s390x 1:3.0.5-2.fc37 fedora 1.8 M p11-kit s390x 0.24.1-3.fc37 fedora 378 k p11-kit-trust s390x 0.24.1-3.fc37 fedora 132 k package-notes-srpm-macros noarch 0.4-16.fc37 fedora 11 k pam s390x 1.5.2-14.fc37 fedora 552 k pam-libs s390x 1.5.2-14.fc37 fedora 56 k pcre s390x 8.45-1.fc37.2 fedora 121 k pcre2 s390x 10.40-1.fc37.1 fedora 219 k pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k perl-srpm-macros noarch 1-46.fc37 fedora 8.3 k pkgconf s390x 1.8.0-3.fc37 fedora 41 k pkgconf-m4 noarch 1.8.0-3.fc37 fedora 14 k pkgconf-pkg-config s390x 1.8.0-3.fc37 fedora 10 k popt s390x 1.19~rc1-3.fc37 fedora 64 k publicsuffix-list-dafsa noarch 20210518-5.fc37 fedora 58 k python-srpm-macros noarch 3.11-4.fc37 fedora 25 k qt5-srpm-macros noarch 5.15.5-2.fc37 fedora 8.1 k readline s390x 8.1-7.fc37 fedora 207 k rpm s390x 4.18.0-0.beta1.4.fc37 fedora 569 k rpm-build-libs s390x 4.18.0-0.beta1.4.fc37 fedora 90 k rpm-libs s390x 4.18.0-0.beta1.4.fc37 fedora 310 k rpmautospec-rpm-macros noarch 0.3.0-1.fc37 fedora 8.8 k rust-srpm-macros noarch 22-1.fc37 fedora 9.5 k setup noarch 2.14.1-2.fc37 fedora 149 k sqlite-libs s390x 3.39.2-2.fc37 fedora 641 k systemd-libs s390x 251.4-51.fc37 fedora 575 k tzdata noarch 2022a-4.fc37 fedora 719 k util-linux-core s390x 2.38.1-1.fc37 fedora 460 k xxhash-libs s390x 0.8.1-3.fc37 fedora 36 k xz-libs s390x 5.2.5-10.fc37 fedora 91 k zip s390x 3.0-33.fc37 fedora 255 k zlib s390x 1.2.12-4.fc37 fedora 95 k zstd s390x 1.5.2-3.fc37 fedora 410 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 152 Packages Total download size: 54 M Installed size: 204 M Downloading Packages: (1/152): ansible-srpm-macros-1-6.fc37.noarch.rp 1.4 kB/s | 7.5 kB 00:05 (2/152): alternatives-1.19-3.fc37.s390x.rpm 6.4 kB/s | 35 kB 00:05 (3/152): audit-libs-3.0.8-3.fc37.s390x.rpm 20 kB/s | 113 kB 00:05 (4/152): authselect-1.4.0-3.fc37.s390x.rpm 339 kB/s | 144 kB 00:00 (5/152): basesystem-11-14.fc37.noarch.rpm 64 kB/s | 7.0 kB 00:00 (6/152): authselect-libs-1.4.0-3.fc37.s390x.rpm 569 kB/s | 245 kB 00:00 (7/152): bash-5.1.16-3.fc37.s390x.rpm 3.2 MB/s | 1.7 MB 00:00 (8/152): binutils-gold-2.38-24.fc38.s390x.rpm 3.4 MB/s | 1.4 MB 00:00 (9/152): bzip2-1.0.8-12.fc37.s390x.rpm 482 kB/s | 51 kB 00:00 (10/152): bzip2-libs-1.0.8-12.fc37.s390x.rpm 400 kB/s | 42 kB 00:00 (11/152): ca-certificates-2022.2.54-5.fc37.noar 5.8 MB/s | 829 kB 00:00 (12/152): coreutils-9.1-6.fc37.s390x.rpm 6.8 MB/s | 1.1 MB 00:00 (13/152): cpio-2.13-13.fc37.s390x.rpm 2.3 MB/s | 272 kB 00:00 (14/152): coreutils-common-9.1-6.fc37.s390x.rpm 11 MB/s | 2.0 MB 00:00 (15/152): binutils-2.38-24.fc38.s390x.rpm 9.8 MB/s | 9.3 MB 00:00 (16/152): cracklib-2.9.6-28.fc36.s390x.rpm 847 kB/s | 91 kB 00:00 (17/152): crypto-policies-20220802-1.gita99dfd2 804 kB/s | 86 kB 00:00 (18/152): curl-7.84.0-2.fc37.s390x.rpm 2.8 MB/s | 310 kB 00:00 (19/152): debugedit-5.0-5.fc37.s390x.rpm 718 kB/s | 76 kB 00:00 (20/152): cyrus-sasl-lib-2.1.28-7.fc37.s390x.rp 5.3 MB/s | 757 kB 00:00 (21/152): diffutils-3.8-3.fc37.s390x.rpm 3.4 MB/s | 377 kB 00:00 (22/152): dwz-0.14-7.fc37.s390x.rpm 1.1 MB/s | 126 kB 00:00 (23/152): ed-1.18-2.fc37.s390x.rpm 721 kB/s | 78 kB 00:00 (24/152): efi-srpm-macros-5-6.fc37.noarch.rpm 213 kB/s | 22 kB 00:00 (25/152): elfutils-0.187-6.fc37.s390x.rpm 4.2 MB/s | 518 kB 00:00 (26/152): elfutils-debuginfod-client-0.187-6.fc 365 kB/s | 39 kB 00:00 (27/152): elfutils-default-yama-scope-0.187-6.f 159 kB/s | 17 kB 00:00 (28/152): elfutils-libelf-0.187-6.fc37.s390x.rp 1.7 MB/s | 197 kB 00:00 (29/152): fedora-gpg-keys-38-0.2.noarch.rpm 1.2 MB/s | 125 kB 00:00 (30/152): elfutils-libs-0.187-6.fc37.s390x.rpm 2.1 MB/s | 253 kB 00:00 (31/152): fedora-release-38-0.2.noarch.rpm 110 kB/s | 12 kB 00:00 (32/152): fedora-release-common-38-0.2.noarch.r 210 kB/s | 22 kB 00:00 (33/152): fedora-release-identity-basic-38-0.2. 117 kB/s | 12 kB 00:00 (34/152): fedora-repos-38-0.2.noarch.rpm 96 kB/s | 10 kB 00:00 (35/152): fedora-repos-rawhide-38-0.2.noarch.rp 92 kB/s | 9.6 kB 00:00 (36/152): file-5.42-4.fc37.s390x.rpm 457 kB/s | 48 kB 00:00 (37/152): file-libs-5.42-4.fc37.s390x.rpm 5.2 MB/s | 675 kB 00:00 (38/152): filesystem-3.18-2.fc37.s390x.rpm 9.2 MB/s | 1.1 MB 00:00 (39/152): findutils-4.9.0-2.fc37.s390x.rpm 3.7 MB/s | 487 kB 00:00 (40/152): fonts-srpm-macros-2.0.5-8.fc37.noarch 249 kB/s | 26 kB 00:00 (41/152): fpc-srpm-macros-1.3-6.fc37.noarch.rpm 74 kB/s | 7.7 kB 00:00 (42/152): gawk-5.1.1-4.fc37.s390x.rpm 6.5 MB/s | 1.0 MB 00:00 (43/152): gdbm-libs-1.23-2.fc37.s390x.rpm 535 kB/s | 56 kB 00:00 (44/152): ghc-srpm-macros-1.5.0-7.fc37.noarch.r 75 kB/s | 7.8 kB 00:00 (45/152): glibc-2.36-1.fc37.s390x.rpm 14 MB/s | 1.7 MB 00:00 (46/152): gdb-minimal-12.1-4.fc37.s390x.rpm 14 MB/s | 3.5 MB 00:00 (47/152): glibc-common-2.36-1.fc37.s390x.rpm 2.9 MB/s | 352 kB 00:00 (48/152): glibc-minimal-langpack-2.36-1.fc37.s3 764 kB/s | 81 kB 00:00 (49/152): gmp-6.2.1-3.fc37.s390x.rpm 2.4 MB/s | 284 kB 00:00 (50/152): glibc-gconv-extra-2.36-1.fc37.s390x.r 7.8 MB/s | 1.6 MB 00:00 (51/152): gnat-srpm-macros-4-16.fc37.noarch.rpm 79 kB/s | 8.3 kB 00:00 (52/152): go-srpm-macros-3.1.0-4.fc37.noarch.rp 255 kB/s | 27 kB 00:00 (53/152): grep-3.7-4.fc37.s390x.rpm 2.2 MB/s | 272 kB 00:00 (54/152): gzip-1.12-2.fc37.s390x.rpm 1.4 MB/s | 166 kB 00:00 (55/152): info-6.8-4.fc37.s390x.rpm 1.9 MB/s | 220 kB 00:00 (56/152): jansson-2.13.1-5.fc37.s390x.rpm 398 kB/s | 42 kB 00:00 (57/152): kernel-srpm-macros-1.0-15.fc37.noarch 89 kB/s | 9.4 kB 00:00 (58/152): keyutils-libs-1.6.1-5.fc37.s390x.rpm 294 kB/s | 31 kB 00:00 (59/152): libacl-2.3.1-4.fc37.s390x.rpm 220 kB/s | 23 kB 00:00 (60/152): krb5-libs-1.19.2-11.fc37.1.s390x.rpm 4.6 MB/s | 706 kB 00:00 (61/152): libarchive-3.6.1-2.fc37.s390x.rpm 3.1 MB/s | 388 kB 00:00 (62/152): libattr-2.5.1-5.fc37.s390x.rpm 169 kB/s | 18 kB 00:00 (63/152): libblkid-2.38.1-1.fc37.s390x.rpm 934 kB/s | 102 kB 00:00 (64/152): libbrotli-1.0.9-9.fc37.s390x.rpm 2.6 MB/s | 317 kB 00:00 (65/152): libcap-2.48-5.fc37.s390x.rpm 628 kB/s | 66 kB 00:00 (66/152): libcap-ng-0.8.3-3.fc37.s390x.rpm 307 kB/s | 32 kB 00:00 (67/152): libcom_err-1.46.5-3.fc37.s390x.rpm 241 kB/s | 25 kB 00:00 (68/152): libcurl-7.84.0-2.fc37.s390x.rpm 2.7 MB/s | 298 kB 00:00 (69/152): libeconf-0.4.0-4.fc37.s390x.rpm 250 kB/s | 26 kB 00:00 (70/152): libdb-5.3.28-53.fc37.s390x.rpm 4.6 MB/s | 720 kB 00:00 (71/152): libevent-2.1.12-7.fc37.s390x.rpm 2.3 MB/s | 252 kB 00:00 (72/152): libfdisk-2.38.1-1.fc37.s390x.rpm 1.4 MB/s | 154 kB 00:00 (73/152): libffi-3.4.2-9.fc37.s390x.rpm 322 kB/s | 34 kB 00:00 (74/152): libgcc-12.1.1-4.fc38.s390x.rpm 751 kB/s | 79 kB 00:00 (75/152): libidn2-2.3.3-2.fc37.s390x.rpm 1.0 MB/s | 113 kB 00:00 (76/152): libgomp-12.1.1-4.fc38.s390x.rpm 2.4 MB/s | 290 kB 00:00 (77/152): libmount-2.38.1-1.fc37.s390x.rpm 1.2 MB/s | 131 kB 00:00 (78/152): libnghttp2-1.48.0-2.fc37.s390x.rpm 672 kB/s | 72 kB 00:00 (79/152): libnsl2-2.0.0-4.fc37.s390x.rpm 282 kB/s | 30 kB 00:00 (80/152): libpkgconf-1.8.0-3.fc37.s390x.rpm 328 kB/s | 34 kB 00:00 (81/152): libpsl-0.21.1-6.fc37.s390x.rpm 589 kB/s | 63 kB 00:00 (82/152): libpwquality-1.4.4-11.fc37.s390x.rpm 1.0 MB/s | 116 kB 00:00 (83/152): libselinux-3.4-5.fc37.s390x.rpm 781 kB/s | 83 kB 00:00 (84/152): libsemanage-3.4-5.fc37.s390x.rpm 1.0 MB/s | 114 kB 00:00 (85/152): libsigsegv-2.14-3.fc37.s390x.rpm 254 kB/s | 27 kB 00:00 (86/152): libsepol-3.4-3.fc37.s390x.rpm 2.5 MB/s | 298 kB 00:00 (87/152): libsmartcols-2.38.1-1.fc37.s390x.rpm 587 kB/s | 63 kB 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3.9 MB/s | 569 kB 00:00 (132/152): rpm-build-libs-4.18.0-0.beta1.4.fc37 841 kB/s | 90 kB 00:00 (133/152): rpm-libs-4.18.0-0.beta1.4.fc37.s390x 2.8 MB/s | 310 kB 00:00 (134/152): rpmautospec-rpm-macros-0.3.0-1.fc37. 84 kB/s | 8.8 kB 00:00 (135/152): rust-srpm-macros-22-1.fc37.noarch.rp 91 kB/s | 9.5 kB 00:00 (136/152): sed-4.8-11.fc37.s390x.rpm 2.7 MB/s | 304 kB 00:00 (137/152): setup-2.14.1-2.fc37.noarch.rpm 1.3 MB/s | 149 kB 00:00 (138/152): shadow-utils-4.11.1-4.fc37.s390x.rpm 7.1 MB/s | 1.1 MB 00:00 (139/152): sqlite-libs-3.39.2-2.fc37.s390x.rpm 5.4 MB/s | 641 kB 00:00 (140/152): systemd-libs-251.4-51.fc37.s390x.rpm 4.0 MB/s | 575 kB 00:00 (141/152): tzdata-2022a-4.fc37.noarch.rpm 6.0 MB/s | 719 kB 00:00 (142/152): tar-1.34-3.fc36.s390x.rpm 5.9 MB/s | 874 kB 00:00 (143/152): unzip-6.0-58.fc37.s390x.rpm 1.5 MB/s | 174 kB 00:00 (144/152): util-linux-core-2.38.1-1.fc37.s390x. 3.6 MB/s | 460 kB 00:00 (145/152): util-linux-2.38.1-1.fc37.s390x.rpm 16 MB/s | 2.3 MB 00:00 (146/152): which-2.21-35.fc37.s390x.rpm 384 kB/s | 41 kB 00:00 (147/152): xxhash-libs-0.8.1-3.fc37.s390x.rpm 344 kB/s | 36 kB 00:00 (148/152): xz-5.2.5-10.fc37.s390x.rpm 2.0 MB/s | 222 kB 00:00 (149/152): xz-libs-5.2.5-10.fc37.s390x.rpm 831 kB/s | 91 kB 00:00 (150/152): zlib-1.2.12-4.fc37.s390x.rpm 901 kB/s | 95 kB 00:00 (151/152): zip-3.0-33.fc37.s390x.rpm 2.1 MB/s | 255 kB 00:00 (152/152): zstd-1.5.2-3.fc37.s390x.rpm 3.1 MB/s | 410 kB 00:00 -------------------------------------------------------------------------------- Total 3.0 MB/s | 54 MB 00:17 fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xEB10B464: Userid : "Fedora (38) " Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464 From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x5323552A: Userid : "Fedora (37) " Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.s390x 1/1 Preparing : 1/1 Installing : libgcc-12.1.1-4.fc38.s390x 1/152 Running scriptlet: libgcc-12.1.1-4.fc38.s390x 1/152 Installing : crypto-policies-20220802-1.gita99dfd2.fc37.noarc 2/152 Running scriptlet: crypto-policies-20220802-1.gita99dfd2.fc37.noarc 2/152 Installing : fedora-release-identity-basic-38-0.2.noarch 3/152 Installing : tzdata-2022a-4.fc37.noarch 4/152 Installing : rust-srpm-macros-22-1.fc37.noarch 5/152 Installing : qt5-srpm-macros-5.15.5-2.fc37.noarch 6/152 Installing : publicsuffix-list-dafsa-20210518-5.fc37.noarch 7/152 Installing : pkgconf-m4-1.8.0-3.fc37.noarch 8/152 Installing : perl-srpm-macros-1-46.fc37.noarch 9/152 Installing : pcre2-syntax-10.40-1.fc37.1.noarch 10/152 Installing : openblas-srpm-macros-2-12.fc37.noarch 11/152 Installing : ocaml-srpm-macros-7-2.fc37.noarch 12/152 Installing : nim-srpm-macros-3-7.fc37.noarch 13/152 Installing : ncurses-base-6.3-3.20220501.fc37.noarch 14/152 Installing : libssh-config-0.9.6-5.fc37.noarch 15/152 Installing : kernel-srpm-macros-1.0-15.fc37.noarch 16/152 Installing : gnat-srpm-macros-4-16.fc37.noarch 17/152 Installing : ghc-srpm-macros-1.5.0-7.fc37.noarch 18/152 Installing : fpc-srpm-macros-1.3-6.fc37.noarch 19/152 Installing : fedora-gpg-keys-38-0.2.noarch 20/152 Installing : fedora-release-38-0.2.noarch 21/152 Installing : fedora-release-common-38-0.2.noarch 22/152 Installing : fedora-repos-rawhide-38-0.2.noarch 23/152 Installing : fedora-repos-38-0.2.noarch 24/152 Installing : setup-2.14.1-2.fc37.noarch 25/152 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.1-2.fc37.noarch 25/152 Installing : filesystem-3.18-2.fc37.s390x 26/152 Installing : basesystem-11-14.fc37.noarch 27/152 Installing : glibc-gconv-extra-2.36-1.fc37.s390x 28/152 Running scriptlet: glibc-gconv-extra-2.36-1.fc37.s390x 28/152 Installing : glibc-minimal-langpack-2.36-1.fc37.s390x 29/152 Installing : 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cracklib-2.9.6-28.fc36.s390x 120/152 Installing : libpwquality-1.4.4-11.fc37.s390x 121/152 Installing : authselect-1.4.0-3.fc37.s390x 122/152 Installing : libnsl2-2.0.0-4.fc37.s390x 123/152 Installing : pam-1.5.2-14.fc37.s390x 124/152 Installing : libssh-0.9.6-5.fc37.s390x 125/152 Installing : libarchive-3.6.1-2.fc37.s390x 126/152 Installing : libevent-2.1.12-7.fc37.s390x 127/152 Installing : openldap-2.6.2-5.fc38.s390x 128/152 Installing : libcurl-7.84.0-2.fc37.s390x 129/152 Installing : elfutils-libs-0.187-6.fc37.s390x 130/152 Installing : elfutils-debuginfod-client-0.187-6.fc37.s390x 131/152 Installing : binutils-gold-2.38-24.fc38.s390x 132/152 Installing : binutils-2.38-24.fc38.s390x 133/152 Running scriptlet: binutils-2.38-24.fc38.s390x 133/152 Installing : elfutils-0.187-6.fc37.s390x 134/152 Installing : gdb-minimal-12.1-4.fc37.s390x 135/152 Installing : debugedit-5.0-5.fc37.s390x 136/152 Installing : curl-7.84.0-2.fc37.s390x 137/152 Running scriptlet: rpm-4.18.0-0.beta1.4.fc37.s390x 138/152 Installing : rpm-4.18.0-0.beta1.4.fc37.s390x 138/152 Installing : rpm-libs-4.18.0-0.beta1.4.fc37.s390x 139/152 Installing : rpm-build-libs-4.18.0-0.beta1.4.fc37.s390x 140/152 Installing : efi-srpm-macros-5-6.fc37.noarch 141/152 Installing : lua-srpm-macros-1-7.fc37.noarch 142/152 Installing : rpmautospec-rpm-macros-0.3.0-1.fc37.noarch 143/152 Installing : ansible-srpm-macros-1-6.fc37.noarch 144/152 Installing : fonts-srpm-macros-1:2.0.5-8.fc37.noarch 145/152 Installing : go-srpm-macros-3.1.0-4.fc37.noarch 146/152 Installing : python-srpm-macros-3.11-4.fc37.noarch 147/152 Installing : redhat-rpm-config-227-1.fc37.noarch 148/152 Installing : rpm-build-4.18.0-0.beta1.4.fc37.s390x 149/152 Installing : util-linux-2.38.1-1.fc37.s390x 150/152 Installing : which-2.21-35.fc37.s390x 151/152 Installing : info-6.8-4.fc37.s390x 152/152 Running scriptlet: filesystem-3.18-2.fc37.s390x 152/152 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 152/152 Running scriptlet: authselect-libs-1.4.0-3.fc37.s390x 152/152 Running scriptlet: rpm-4.18.0-0.beta1.4.fc37.s390x 152/152 Running scriptlet: info-6.8-4.fc37.s390x 152/152 Verifying : alternatives-1.19-3.fc37.s390x 1/152 Verifying : ansible-srpm-macros-1-6.fc37.noarch 2/152 Verifying : audit-libs-3.0.8-3.fc37.s390x 3/152 Verifying : authselect-1.4.0-3.fc37.s390x 4/152 Verifying : authselect-libs-1.4.0-3.fc37.s390x 5/152 Verifying : basesystem-11-14.fc37.noarch 6/152 Verifying : bash-5.1.16-3.fc37.s390x 7/152 Verifying : binutils-2.38-24.fc38.s390x 8/152 Verifying : binutils-gold-2.38-24.fc38.s390x 9/152 Verifying : bzip2-1.0.8-12.fc37.s390x 10/152 Verifying : bzip2-libs-1.0.8-12.fc37.s390x 11/152 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 12/152 Verifying : coreutils-9.1-6.fc37.s390x 13/152 Verifying : coreutils-common-9.1-6.fc37.s390x 14/152 Verifying : cpio-2.13-13.fc37.s390x 15/152 Verifying : cracklib-2.9.6-28.fc36.s390x 16/152 Verifying : crypto-policies-20220802-1.gita99dfd2.fc37.noarc 17/152 Verifying : curl-7.84.0-2.fc37.s390x 18/152 Verifying : cyrus-sasl-lib-2.1.28-7.fc37.s390x 19/152 Verifying : debugedit-5.0-5.fc37.s390x 20/152 Verifying : diffutils-3.8-3.fc37.s390x 21/152 Verifying : dwz-0.14-7.fc37.s390x 22/152 Verifying : ed-1.18-2.fc37.s390x 23/152 Verifying : efi-srpm-macros-5-6.fc37.noarch 24/152 Verifying : elfutils-0.187-6.fc37.s390x 25/152 Verifying : elfutils-debuginfod-client-0.187-6.fc37.s390x 26/152 Verifying : elfutils-default-yama-scope-0.187-6.fc37.noarch 27/152 Verifying : elfutils-libelf-0.187-6.fc37.s390x 28/152 Verifying : elfutils-libs-0.187-6.fc37.s390x 29/152 Verifying : fedora-gpg-keys-38-0.2.noarch 30/152 Verifying : fedora-release-38-0.2.noarch 31/152 Verifying : fedora-release-common-38-0.2.noarch 32/152 Verifying : fedora-release-identity-basic-38-0.2.noarch 33/152 Verifying : fedora-repos-38-0.2.noarch 34/152 Verifying : fedora-repos-rawhide-38-0.2.noarch 35/152 Verifying : file-5.42-4.fc37.s390x 36/152 Verifying : file-libs-5.42-4.fc37.s390x 37/152 Verifying : filesystem-3.18-2.fc37.s390x 38/152 Verifying : findutils-1:4.9.0-2.fc37.s390x 39/152 Verifying : fonts-srpm-macros-1:2.0.5-8.fc37.noarch 40/152 Verifying : fpc-srpm-macros-1.3-6.fc37.noarch 41/152 Verifying : gawk-5.1.1-4.fc37.s390x 42/152 Verifying : gdb-minimal-12.1-4.fc37.s390x 43/152 Verifying : gdbm-libs-1:1.23-2.fc37.s390x 44/152 Verifying : ghc-srpm-macros-1.5.0-7.fc37.noarch 45/152 Verifying : glibc-2.36-1.fc37.s390x 46/152 Verifying : glibc-common-2.36-1.fc37.s390x 47/152 Verifying : glibc-gconv-extra-2.36-1.fc37.s390x 48/152 Verifying : glibc-minimal-langpack-2.36-1.fc37.s390x 49/152 Verifying : gmp-1:6.2.1-3.fc37.s390x 50/152 Verifying : gnat-srpm-macros-4-16.fc37.noarch 51/152 Verifying : go-srpm-macros-3.1.0-4.fc37.noarch 52/152 Verifying : grep-3.7-4.fc37.s390x 53/152 Verifying : gzip-1.12-2.fc37.s390x 54/152 Verifying : info-6.8-4.fc37.s390x 55/152 Verifying : jansson-2.13.1-5.fc37.s390x 56/152 Verifying : kernel-srpm-macros-1.0-15.fc37.noarch 57/152 Verifying : keyutils-libs-1.6.1-5.fc37.s390x 58/152 Verifying : krb5-libs-1.19.2-11.fc37.1.s390x 59/152 Verifying : libacl-2.3.1-4.fc37.s390x 60/152 Verifying : libarchive-3.6.1-2.fc37.s390x 61/152 Verifying : libattr-2.5.1-5.fc37.s390x 62/152 Verifying : libblkid-2.38.1-1.fc37.s390x 63/152 Verifying : libbrotli-1.0.9-9.fc37.s390x 64/152 Verifying : libcap-2.48-5.fc37.s390x 65/152 Verifying : libcap-ng-0.8.3-3.fc37.s390x 66/152 Verifying : libcom_err-1.46.5-3.fc37.s390x 67/152 Verifying : libcurl-7.84.0-2.fc37.s390x 68/152 Verifying : libdb-5.3.28-53.fc37.s390x 69/152 Verifying : libeconf-0.4.0-4.fc37.s390x 70/152 Verifying : libevent-2.1.12-7.fc37.s390x 71/152 Verifying : libfdisk-2.38.1-1.fc37.s390x 72/152 Verifying : libffi-3.4.2-9.fc37.s390x 73/152 Verifying : libgcc-12.1.1-4.fc38.s390x 74/152 Verifying : libgomp-12.1.1-4.fc38.s390x 75/152 Verifying : libidn2-2.3.3-2.fc37.s390x 76/152 Verifying : libmount-2.38.1-1.fc37.s390x 77/152 Verifying : libnghttp2-1.48.0-2.fc37.s390x 78/152 Verifying : libnsl2-2.0.0-4.fc37.s390x 79/152 Verifying : libpkgconf-1.8.0-3.fc37.s390x 80/152 Verifying : libpsl-0.21.1-6.fc37.s390x 81/152 Verifying : libpwquality-1.4.4-11.fc37.s390x 82/152 Verifying : libselinux-3.4-5.fc37.s390x 83/152 Verifying : libsemanage-3.4-5.fc37.s390x 84/152 Verifying : libsepol-3.4-3.fc37.s390x 85/152 Verifying : libsigsegv-2.14-3.fc37.s390x 86/152 Verifying : libsmartcols-2.38.1-1.fc37.s390x 87/152 Verifying : libssh-0.9.6-5.fc37.s390x 88/152 Verifying : libssh-config-0.9.6-5.fc37.noarch 89/152 Verifying : libstdc++-12.1.1-4.fc38.s390x 90/152 Verifying : libtasn1-4.18.0-3.fc37.s390x 91/152 Verifying : libtirpc-1.3.3-0.fc37.s390x 92/152 Verifying : libunistring-1.0-2.fc37.s390x 93/152 Verifying : libutempter-1.2.1-7.fc37.s390x 94/152 Verifying : libuuid-2.38.1-1.fc37.s390x 95/152 Verifying : libverto-0.3.2-4.fc37.s390x 96/152 Verifying : libxcrypt-4.4.28-3.fc38.s390x 97/152 Verifying : libxml2-2.9.14-3.fc37.s390x 98/152 Verifying : libzstd-1.5.2-3.fc37.s390x 99/152 Verifying : lua-libs-5.4.4-4.fc37.s390x 100/152 Verifying : lua-srpm-macros-1-7.fc37.noarch 101/152 Verifying : lz4-libs-1.9.3-5.fc37.s390x 102/152 Verifying : mpfr-4.1.0-10.fc37.s390x 103/152 Verifying : ncurses-base-6.3-3.20220501.fc37.noarch 104/152 Verifying : ncurses-libs-6.3-3.20220501.fc37.s390x 105/152 Verifying : nim-srpm-macros-3-7.fc37.noarch 106/152 Verifying : ocaml-srpm-macros-7-2.fc37.noarch 107/152 Verifying : openblas-srpm-macros-2-12.fc37.noarch 108/152 Verifying : openldap-2.6.2-5.fc38.s390x 109/152 Verifying : openssl-libs-1:3.0.5-2.fc37.s390x 110/152 Verifying : p11-kit-0.24.1-3.fc37.s390x 111/152 Verifying : p11-kit-trust-0.24.1-3.fc37.s390x 112/152 Verifying : package-notes-srpm-macros-0.4-16.fc37.noarch 113/152 Verifying : pam-1.5.2-14.fc37.s390x 114/152 Verifying : pam-libs-1.5.2-14.fc37.s390x 115/152 Verifying : patch-2.7.6-17.fc37.s390x 116/152 Verifying : pcre-8.45-1.fc37.2.s390x 117/152 Verifying : pcre2-10.40-1.fc37.1.s390x 118/152 Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 119/152 Verifying : perl-srpm-macros-1-46.fc37.noarch 120/152 Verifying : pkgconf-1.8.0-3.fc37.s390x 121/152 Verifying : pkgconf-m4-1.8.0-3.fc37.noarch 122/152 Verifying : pkgconf-pkg-config-1.8.0-3.fc37.s390x 123/152 Verifying : popt-1.19~rc1-3.fc37.s390x 124/152 Verifying : publicsuffix-list-dafsa-20210518-5.fc37.noarch 125/152 Verifying : python-srpm-macros-3.11-4.fc37.noarch 126/152 Verifying : qt5-srpm-macros-5.15.5-2.fc37.noarch 127/152 Verifying : readline-8.1-7.fc37.s390x 128/152 Verifying : redhat-rpm-config-227-1.fc37.noarch 129/152 Verifying : rpm-4.18.0-0.beta1.4.fc37.s390x 130/152 Verifying : rpm-build-4.18.0-0.beta1.4.fc37.s390x 131/152 Verifying : rpm-build-libs-4.18.0-0.beta1.4.fc37.s390x 132/152 Verifying : rpm-libs-4.18.0-0.beta1.4.fc37.s390x 133/152 Verifying : rpmautospec-rpm-macros-0.3.0-1.fc37.noarch 134/152 Verifying : rust-srpm-macros-22-1.fc37.noarch 135/152 Verifying : sed-4.8-11.fc37.s390x 136/152 Verifying : setup-2.14.1-2.fc37.noarch 137/152 Verifying : shadow-utils-2:4.11.1-4.fc37.s390x 138/152 Verifying : sqlite-libs-3.39.2-2.fc37.s390x 139/152 Verifying : systemd-libs-251.4-51.fc37.s390x 140/152 Verifying : tar-2:1.34-3.fc36.s390x 141/152 Verifying : tzdata-2022a-4.fc37.noarch 142/152 Verifying : unzip-6.0-58.fc37.s390x 143/152 Verifying : util-linux-2.38.1-1.fc37.s390x 144/152 Verifying : util-linux-core-2.38.1-1.fc37.s390x 145/152 Verifying : which-2.21-35.fc37.s390x 146/152 Verifying : xxhash-libs-0.8.1-3.fc37.s390x 147/152 Verifying : xz-5.2.5-10.fc37.s390x 148/152 Verifying : xz-libs-5.2.5-10.fc37.s390x 149/152 Verifying : zip-3.0-33.fc37.s390x 150/152 Verifying : zlib-1.2.12-4.fc37.s390x 151/152 Verifying : zstd-1.5.2-3.fc37.s390x 152/152 Installed products updated. Installed: alternatives-1.19-3.fc37.s390x ansible-srpm-macros-1-6.fc37.noarch audit-libs-3.0.8-3.fc37.s390x authselect-1.4.0-3.fc37.s390x authselect-libs-1.4.0-3.fc37.s390x basesystem-11-14.fc37.noarch bash-5.1.16-3.fc37.s390x binutils-2.38-24.fc38.s390x binutils-gold-2.38-24.fc38.s390x bzip2-1.0.8-12.fc37.s390x bzip2-libs-1.0.8-12.fc37.s390x ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-6.fc37.s390x coreutils-common-9.1-6.fc37.s390x cpio-2.13-13.fc37.s390x cracklib-2.9.6-28.fc36.s390x crypto-policies-20220802-1.gita99dfd2.fc37.noarch curl-7.84.0-2.fc37.s390x cyrus-sasl-lib-2.1.28-7.fc37.s390x debugedit-5.0-5.fc37.s390x diffutils-3.8-3.fc37.s390x dwz-0.14-7.fc37.s390x ed-1.18-2.fc37.s390x efi-srpm-macros-5-6.fc37.noarch elfutils-0.187-6.fc37.s390x elfutils-debuginfod-client-0.187-6.fc37.s390x elfutils-default-yama-scope-0.187-6.fc37.noarch elfutils-libelf-0.187-6.fc37.s390x elfutils-libs-0.187-6.fc37.s390x fedora-gpg-keys-38-0.2.noarch fedora-release-38-0.2.noarch fedora-release-common-38-0.2.noarch fedora-release-identity-basic-38-0.2.noarch fedora-repos-38-0.2.noarch fedora-repos-rawhide-38-0.2.noarch file-5.42-4.fc37.s390x file-libs-5.42-4.fc37.s390x filesystem-3.18-2.fc37.s390x findutils-1:4.9.0-2.fc37.s390x fonts-srpm-macros-1:2.0.5-8.fc37.noarch fpc-srpm-macros-1.3-6.fc37.noarch gawk-5.1.1-4.fc37.s390x gdb-minimal-12.1-4.fc37.s390x gdbm-libs-1:1.23-2.fc37.s390x ghc-srpm-macros-1.5.0-7.fc37.noarch glibc-2.36-1.fc37.s390x glibc-common-2.36-1.fc37.s390x glibc-gconv-extra-2.36-1.fc37.s390x glibc-minimal-langpack-2.36-1.fc37.s390x gmp-1:6.2.1-3.fc37.s390x gnat-srpm-macros-4-16.fc37.noarch go-srpm-macros-3.1.0-4.fc37.noarch grep-3.7-4.fc37.s390x gzip-1.12-2.fc37.s390x info-6.8-4.fc37.s390x jansson-2.13.1-5.fc37.s390x kernel-srpm-macros-1.0-15.fc37.noarch keyutils-libs-1.6.1-5.fc37.s390x krb5-libs-1.19.2-11.fc37.1.s390x libacl-2.3.1-4.fc37.s390x libarchive-3.6.1-2.fc37.s390x libattr-2.5.1-5.fc37.s390x libblkid-2.38.1-1.fc37.s390x libbrotli-1.0.9-9.fc37.s390x libcap-2.48-5.fc37.s390x libcap-ng-0.8.3-3.fc37.s390x libcom_err-1.46.5-3.fc37.s390x libcurl-7.84.0-2.fc37.s390x libdb-5.3.28-53.fc37.s390x libeconf-0.4.0-4.fc37.s390x libevent-2.1.12-7.fc37.s390x libfdisk-2.38.1-1.fc37.s390x libffi-3.4.2-9.fc37.s390x libgcc-12.1.1-4.fc38.s390x libgomp-12.1.1-4.fc38.s390x libidn2-2.3.3-2.fc37.s390x libmount-2.38.1-1.fc37.s390x libnghttp2-1.48.0-2.fc37.s390x libnsl2-2.0.0-4.fc37.s390x libpkgconf-1.8.0-3.fc37.s390x libpsl-0.21.1-6.fc37.s390x libpwquality-1.4.4-11.fc37.s390x libselinux-3.4-5.fc37.s390x libsemanage-3.4-5.fc37.s390x libsepol-3.4-3.fc37.s390x libsigsegv-2.14-3.fc37.s390x libsmartcols-2.38.1-1.fc37.s390x libssh-0.9.6-5.fc37.s390x libssh-config-0.9.6-5.fc37.noarch libstdc++-12.1.1-4.fc38.s390x libtasn1-4.18.0-3.fc37.s390x libtirpc-1.3.3-0.fc37.s390x libunistring-1.0-2.fc37.s390x libutempter-1.2.1-7.fc37.s390x libuuid-2.38.1-1.fc37.s390x libverto-0.3.2-4.fc37.s390x libxcrypt-4.4.28-3.fc38.s390x libxml2-2.9.14-3.fc37.s390x libzstd-1.5.2-3.fc37.s390x lua-libs-5.4.4-4.fc37.s390x lua-srpm-macros-1-7.fc37.noarch lz4-libs-1.9.3-5.fc37.s390x mpfr-4.1.0-10.fc37.s390x ncurses-base-6.3-3.20220501.fc37.noarch ncurses-libs-6.3-3.20220501.fc37.s390x nim-srpm-macros-3-7.fc37.noarch ocaml-srpm-macros-7-2.fc37.noarch openblas-srpm-macros-2-12.fc37.noarch openldap-2.6.2-5.fc38.s390x openssl-libs-1:3.0.5-2.fc37.s390x p11-kit-0.24.1-3.fc37.s390x p11-kit-trust-0.24.1-3.fc37.s390x package-notes-srpm-macros-0.4-16.fc37.noarch pam-1.5.2-14.fc37.s390x pam-libs-1.5.2-14.fc37.s390x patch-2.7.6-17.fc37.s390x pcre-8.45-1.fc37.2.s390x pcre2-10.40-1.fc37.1.s390x pcre2-syntax-10.40-1.fc37.1.noarch perl-srpm-macros-1-46.fc37.noarch pkgconf-1.8.0-3.fc37.s390x pkgconf-m4-1.8.0-3.fc37.noarch pkgconf-pkg-config-1.8.0-3.fc37.s390x popt-1.19~rc1-3.fc37.s390x publicsuffix-list-dafsa-20210518-5.fc37.noarch python-srpm-macros-3.11-4.fc37.noarch qt5-srpm-macros-5.15.5-2.fc37.noarch readline-8.1-7.fc37.s390x redhat-rpm-config-227-1.fc37.noarch rpm-4.18.0-0.beta1.4.fc37.s390x rpm-build-4.18.0-0.beta1.4.fc37.s390x rpm-build-libs-4.18.0-0.beta1.4.fc37.s390x rpm-libs-4.18.0-0.beta1.4.fc37.s390x rpmautospec-rpm-macros-0.3.0-1.fc37.noarch rust-srpm-macros-22-1.fc37.noarch sed-4.8-11.fc37.s390x setup-2.14.1-2.fc37.noarch shadow-utils-2:4.11.1-4.fc37.s390x sqlite-libs-3.39.2-2.fc37.s390x systemd-libs-251.4-51.fc37.s390x tar-2:1.34-3.fc36.s390x tzdata-2022a-4.fc37.noarch unzip-6.0-58.fc37.s390x util-linux-2.38.1-1.fc37.s390x util-linux-core-2.38.1-1.fc37.s390x which-2.21-35.fc37.s390x xxhash-libs-0.8.1-3.fc37.s390x xz-5.2.5-10.fc37.s390x xz-libs-5.2.5-10.fc37.s390x zip-3.0-33.fc37.s390x zlib-1.2.12-4.fc37.s390x zstd-1.5.2-3.fc37.s390x Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: tzdata-2022a-4.fc37.noarch glibc-common-2.36-1.fc37.s390x popt-1.19~rc1-3.fc37.s390x binutils-2.38-24.fc38.s390x libssh-config-0.9.6-5.fc37.noarch lz4-libs-1.9.3-5.fc37.s390x coreutils-9.1-6.fc37.s390x rpm-4.18.0-0.beta1.4.fc37.s390x go-srpm-macros-3.1.0-4.fc37.noarch libsemanage-3.4-5.fc37.s390x p11-kit-trust-0.24.1-3.fc37.s390x sqlite-libs-3.39.2-2.fc37.s390x lua-srpm-macros-1-7.fc37.noarch bzip2-1.0.8-12.fc37.s390x libzstd-1.5.2-3.fc37.s390x dwz-0.14-7.fc37.s390x xz-5.2.5-10.fc37.s390x grep-3.7-4.fc37.s390x binutils-gold-2.38-24.fc38.s390x authselect-1.4.0-3.fc37.s390x libtasn1-4.18.0-3.fc37.s390x gmp-6.2.1-3.fc37.s390x fedora-repos-38-0.2.noarch libidn2-2.3.3-2.fc37.s390x libbrotli-1.0.9-9.fc37.s390x libxml2-2.9.14-3.fc37.s390x elfutils-libs-0.187-6.fc37.s390x publicsuffix-list-dafsa-20210518-5.fc37.noarch libselinux-3.4-5.fc37.s390x zlib-1.2.12-4.fc37.s390x mpfr-4.1.0-10.fc37.s390x bash-5.1.16-3.fc37.s390x ocaml-srpm-macros-7-2.fc37.noarch systemd-libs-251.4-51.fc37.s390x patch-2.7.6-17.fc37.s390x kernel-srpm-macros-1.0-15.fc37.noarch sed-4.8-11.fc37.s390x rpm-build-4.18.0-0.beta1.4.fc37.s390x filesystem-3.18-2.fc37.s390x gdbm-libs-1.23-2.fc37.s390x libpkgconf-1.8.0-3.fc37.s390x lua-libs-5.4.4-4.fc37.s390x gpg-pubkey-eb10b464-6202d9c6 xz-libs-5.2.5-10.fc37.s390x libpsl-0.21.1-6.fc37.s390x libcap-ng-0.8.3-3.fc37.s390x fedora-release-38-0.2.noarch cracklib-2.9.6-28.fc36.s390x setup-2.14.1-2.fc37.noarch nim-srpm-macros-3-7.fc37.noarch libunistring-1.0-2.fc37.s390x qt5-srpm-macros-5.15.5-2.fc37.noarch gawk-5.1.1-4.fc37.s390x glibc-gconv-extra-2.36-1.fc37.s390x pcre2-syntax-10.40-1.fc37.1.noarch libgcc-12.1.1-4.fc38.s390x shadow-utils-4.11.1-4.fc37.s390x rpm-build-libs-4.18.0-0.beta1.4.fc37.s390x findutils-4.9.0-2.fc37.s390x glibc-minimal-langpack-2.36-1.fc37.s390x coreutils-common-9.1-6.fc37.s390x ca-certificates-2022.2.54-5.fc37.noarch pam-1.5.2-14.fc37.s390x libeconf-0.4.0-4.fc37.s390x basesystem-11-14.fc37.noarch alternatives-1.19-3.fc37.s390x fedora-release-common-38-0.2.noarch libpwquality-1.4.4-11.fc37.s390x ed-1.18-2.fc37.s390x gnat-srpm-macros-4-16.fc37.noarch fonts-srpm-macros-2.0.5-8.fc37.noarch libxcrypt-4.4.28-3.fc38.s390x perl-srpm-macros-1-46.fc37.noarch libcap-2.48-5.fc37.s390x gpg-pubkey-5323552a-6112bcdc ghc-srpm-macros-1.5.0-7.fc37.noarch libattr-2.5.1-5.fc37.s390x file-libs-5.42-4.fc37.s390x p11-kit-0.24.1-3.fc37.s390x libcurl-7.84.0-2.fc37.s390x python-srpm-macros-3.11-4.fc37.noarch file-5.42-4.fc37.s390x pam-libs-1.5.2-14.fc37.s390x libsepol-3.4-3.fc37.s390x gdb-minimal-12.1-4.fc37.s390x fedora-repos-rawhide-38-0.2.noarch tar-1.34-3.fc36.s390x glibc-2.36-1.fc37.s390x libutempter-1.2.1-7.fc37.s390x package-notes-srpm-macros-0.4-16.fc37.noarch libblkid-2.38.1-1.fc37.s390x libnsl2-2.0.0-4.fc37.s390x libssh-0.9.6-5.fc37.s390x elfutils-debuginfod-client-0.187-6.fc37.s390x redhat-rpm-config-227-1.fc37.noarch libarchive-3.6.1-2.fc37.s390x krb5-libs-1.19.2-11.fc37.1.s390x which-2.21-35.fc37.s390x xxhash-libs-0.8.1-3.fc37.s390x libcom_err-1.46.5-3.fc37.s390x readline-8.1-7.fc37.s390x debugedit-5.0-5.fc37.s390x fedora-release-identity-basic-38-0.2.noarch openssl-libs-3.0.5-2.fc37.s390x pcre-8.45-1.fc37.2.s390x libmount-2.38.1-1.fc37.s390x unzip-6.0-58.fc37.s390x bzip2-libs-1.0.8-12.fc37.s390x crypto-policies-20220802-1.gita99dfd2.fc37.noarch pkgconf-m4-1.8.0-3.fc37.noarch libtirpc-1.3.3-0.fc37.s390x zip-3.0-33.fc37.s390x pcre2-10.40-1.fc37.1.s390x keyutils-libs-1.6.1-5.fc37.s390x info-6.8-4.fc37.s390x cpio-2.13-13.fc37.s390x pkgconf-pkg-config-1.8.0-3.fc37.s390x libdb-5.3.28-53.fc37.s390x libnghttp2-1.48.0-2.fc37.s390x libsmartcols-2.38.1-1.fc37.s390x util-linux-2.38.1-1.fc37.s390x authselect-libs-1.4.0-3.fc37.s390x rpmautospec-rpm-macros-0.3.0-1.fc37.noarch libgomp-12.1.1-4.fc38.s390x libstdc++-12.1.1-4.fc38.s390x cyrus-sasl-lib-2.1.28-7.fc37.s390x rust-srpm-macros-22-1.fc37.noarch jansson-2.13.1-5.fc37.s390x curl-7.84.0-2.fc37.s390x ncurses-libs-6.3-3.20220501.fc37.s390x gzip-1.12-2.fc37.s390x fedora-gpg-keys-38-0.2.noarch rpm-libs-4.18.0-0.beta1.4.fc37.s390x efi-srpm-macros-5-6.fc37.noarch libacl-2.3.1-4.fc37.s390x util-linux-core-2.38.1-1.fc37.s390x audit-libs-3.0.8-3.fc37.s390x pkgconf-1.8.0-3.fc37.s390x libverto-0.3.2-4.fc37.s390x libfdisk-2.38.1-1.fc37.s390x openblas-srpm-macros-2-12.fc37.noarch zstd-1.5.2-3.fc37.s390x libuuid-2.38.1-1.fc37.s390x fpc-srpm-macros-1.3-6.fc37.noarch elfutils-default-yama-scope-0.187-6.fc37.noarch openldap-2.6.2-5.fc38.s390x diffutils-3.8-3.fc37.s390x elfutils-libelf-0.187-6.fc37.s390x libffi-3.4.2-9.fc37.s390x libsigsegv-2.14-3.fc37.s390x libevent-2.1.12-7.fc37.s390x ansible-srpm-macros-1-6.fc37.noarch elfutils-0.187-6.fc37.s390x ncurses-base-6.3-3.20220501.fc37.noarch Start: buildsrpm Start: rpmbuild -bs Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1660521600 Wrote: /builddir/build/SRPMS/samtools-1.15.1-1.fc38.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-s390x-1660573664.597255/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-s390x-1660573664.597255/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-s390x-1660573664.597255/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-rabtnn8f/samtools/samtools.spec) Config(child) 1 minutes 19 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 (timeout=18000): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/samtools-1.15.1-1.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1660573664.597255 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.1 starting (python version = 3.10.4, NVR = mock-3.1-1.fc35)... 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/results/samtools-1.15.1-1.fc38.src.rpm) Config(fedora-rawhide-s390x) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1660573664.597255/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 Mock Version: 3.1 INFO: Mock Version: 3.1 Start: dnf update 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 593 B/s | 3.3 kB 00:05 fedora 1.0 kB/s | 5.9 kB 00:05 fedora 93 kB/s | 1.7 MB 00:18 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for samtools-1.15.1-1.fc38.src.rpm Start: build setup for samtools-1.15.1-1.fc38.src.rpm Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1660521600 Wrote: /builddir/build/SRPMS/samtools-1.15.1-1.fc38.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 314 B/s | 3.3 kB 00:10 fedora 1.0 kB/s | 5.9 kB 00:05 fedora 97 kB/s | 1.7 MB 00:17 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: gcc s390x 12.1.1-4.fc38 fedora 25 M htslib-devel s390x 1.15.1-1.fc38 copr_base 100 k htslib-tools s390x 1.15.1-1.fc38 copr_base 515 k make s390x 1:4.3-11.fc37 fedora 536 k ncurses-devel s390x 6.3-3.20220501.fc37 fedora 547 k perl-FindBin noarch 1.53-491.fc37 fedora 18 k perl-Getopt-Long noarch 1:2.52-489.fc37 fedora 60 k perl-interpreter s390x 4:5.36.0-491.fc37 fedora 76 k perl-lib s390x 0.65-491.fc37 fedora 19 k zlib-devel s390x 1.2.12-4.fc37 fedora 44 k Installing dependencies: annobin-docs noarch 10.81-1.fc38 fedora 91 k annobin-plugin-gcc s390x 10.81-1.fc38 fedora 880 k cpp s390x 12.1.1-4.fc38 fedora 7.7 M gc s390x 8.0.6-4.fc37 fedora 98 k gcc-plugin-annobin s390x 12.1.1-4.fc38 fedora 48 k glibc-devel s390x 2.36-1.fc37 fedora 104 k glibc-headers-s390 noarch 2.36-1.fc37 fedora 565 k groff-base s390x 1.22.4-10.fc37 fedora 1.0 M guile22 s390x 2.2.7-6.fc37 fedora 6.5 M htslib s390x 1.15.1-1.fc38 copr_base 474 k kernel-headers s390x 5.19.0-1.fc37 fedora 1.5 M libasan s390x 12.1.1-4.fc38 fedora 421 k libatomic s390x 12.1.1-4.fc38 fedora 39 k libmpc s390x 1.2.1-5.fc37 fedora 61 k libtool-ltdl s390x 2.4.7-2.fc37 fedora 36 k libubsan s390x 12.1.1-4.fc38 fedora 190 k libxcrypt-devel s390x 4.4.28-3.fc38 fedora 28 k ncurses s390x 6.3-3.20220501.fc37 fedora 409 k ncurses-c++-libs s390x 6.3-3.20220501.fc37 fedora 36 k perl-Carp noarch 1.52-489.fc37 fedora 29 k perl-Class-Struct noarch 0.66-491.fc37 fedora 26 k perl-DynaLoader s390x 1.52-491.fc37 fedora 30 k perl-Encode s390x 4:3.19-491.fc37 fedora 1.7 M perl-Errno s390x 1.36-491.fc37 fedora 19 k perl-Exporter noarch 5.77-489.fc37 fedora 31 k perl-Fcntl s390x 1.15-491.fc37 fedora 25 k perl-File-Basename noarch 2.85-491.fc37 fedora 22 k perl-File-Path noarch 2.18-489.fc37 fedora 35 k perl-File-Temp noarch 1:0.231.100-489.fc37 fedora 59 k perl-File-stat noarch 1.12-491.fc37 fedora 22 k perl-Getopt-Std noarch 1.13-491.fc37 fedora 20 k perl-HTTP-Tiny noarch 0.082-1.fc37 fedora 55 k perl-IO s390x 1.50-491.fc37 fedora 96 k perl-IPC-Open3 noarch 1.22-491.fc37 fedora 27 k perl-MIME-Base64 s390x 3.16-489.fc37 fedora 30 k perl-POSIX s390x 2.03-491.fc37 fedora 101 k perl-PathTools s390x 3.84-489.fc37 fedora 89 k perl-Pod-Escapes noarch 1:1.07-489.fc37 fedora 20 k perl-Pod-Perldoc noarch 3.28.01-490.fc37 fedora 90 k perl-Pod-Simple noarch 1:3.43-490.fc37 fedora 225 k perl-Pod-Usage noarch 4:2.03-3.fc37 fedora 40 k perl-Scalar-List-Utils s390x 5:1.63-489.fc38 fedora 71 k perl-SelectSaver noarch 1.02-491.fc37 fedora 16 k perl-Socket s390x 4:2.035-2.fc37 fedora 55 k perl-Storable s390x 1:3.26-489.fc37 fedora 93 k perl-Symbol noarch 1.09-491.fc37 fedora 19 k perl-Term-ANSIColor noarch 5.01-490.fc37 fedora 48 k perl-Term-Cap noarch 1.17-489.fc37 fedora 22 k perl-Text-ParseWords noarch 3.31-489.fc37 fedora 16 k perl-Text-Tabs+Wrap noarch 2021.0814-489.fc37 fedora 22 k perl-Time-Local noarch 2:1.300-489.fc37 fedora 33 k perl-constant noarch 1.33-490.fc37 fedora 23 k perl-if noarch 0.61.000-491.fc37 fedora 18 k perl-libs s390x 4:5.36.0-491.fc37 fedora 2.2 M perl-mro s390x 1.26-491.fc37 fedora 33 k perl-overload noarch 1.35-491.fc37 fedora 50 k perl-overloading noarch 0.02-491.fc37 fedora 17 k perl-parent noarch 1:0.238-489.fc37 fedora 14 k perl-podlators noarch 1:4.14-489.fc37 fedora 116 k perl-subs noarch 1.04-491.fc37 fedora 16 k perl-vars noarch 1.05-491.fc37 fedora 17 k Transaction Summary ================================================================================ Install 71 Packages Total download size: 53 M Installed size: 175 M Downloading Packages: (1/71): htslib-devel-1.15.1-1.fc38.s390x.rpm 17 kB/s | 100 kB 00:05 (2/71): htslib-1.15.1-1.fc38.s390x.rpm 80 kB/s | 474 kB 00:05 (3/71): htslib-tools-1.15.1-1.fc38.s390x.rpm 80 kB/s | 515 kB 00:06 (4/71): annobin-docs-10.81-1.fc38.noarch.rpm 16 kB/s | 91 kB 00:05 (5/71): gc-8.0.6-4.fc37.s390x.rpm 654 kB/s | 98 kB 00:00 (6/71): annobin-plugin-gcc-10.81-1.fc38.s390x.r 134 kB/s | 880 kB 00:06 (7/71): gcc-plugin-annobin-12.1.1-4.fc38.s390x. 314 kB/s | 48 kB 00:00 (8/71): cpp-12.1.1-4.fc38.s390x.rpm 1.2 MB/s | 7.7 MB 00:06 (9/71): glibc-devel-2.36-1.fc37.s390x.rpm 673 kB/s | 104 kB 00:00 (10/71): glibc-headers-s390-2.36-1.fc37.noarch. 3.5 MB/s | 565 kB 00:00 (11/71): guile22-2.2.7-6.fc37.s390x.rpm 10 MB/s | 6.5 MB 00:00 (12/71): kernel-headers-5.19.0-1.fc37.s390x.rpm 8.7 MB/s | 1.5 MB 00:00 (13/71): groff-base-1.22.4-10.fc37.s390x.rpm 1.1 MB/s | 1.0 MB 00:00 (14/71): libasan-12.1.1-4.fc38.s390x.rpm 2.7 MB/s | 421 kB 00:00 (15/71): libatomic-12.1.1-4.fc38.s390x.rpm 251 kB/s | 39 kB 00:00 (16/71): libmpc-1.2.1-5.fc37.s390x.rpm 413 kB/s | 61 kB 00:00 (17/71): libtool-ltdl-2.4.7-2.fc37.s390x.rpm 235 kB/s | 36 kB 00:00 (18/71): libubsan-12.1.1-4.fc38.s390x.rpm 1.2 MB/s | 190 kB 00:00 (19/71): libxcrypt-devel-4.4.28-3.fc38.s390x.rp 178 kB/s | 28 kB 00:00 (20/71): make-4.3-11.fc37.s390x.rpm 3.4 MB/s | 536 kB 00:00 (21/71): ncurses-c++-libs-6.3-3.20220501.fc37.s 223 kB/s | 36 kB 00:00 (22/71): ncurses-devel-6.3-3.20220501.fc37.s390 3.0 MB/s | 547 kB 00:00 (23/71): ncurses-6.3-3.20220501.fc37.s390x.rpm 890 kB/s | 409 kB 00:00 (24/71): gcc-12.1.1-4.fc38.s390x.rpm 8.3 MB/s | 25 MB 00:03 (25/71): perl-Carp-1.52-489.fc37.noarch.rpm 195 kB/s | 29 kB 00:00 (26/71): perl-Class-Struct-0.66-491.fc37.noarch 173 kB/s | 26 kB 00:00 (27/71): perl-DynaLoader-1.52-491.fc37.s390x.rp 205 kB/s | 30 kB 00:00 (28/71): perl-Errno-1.36-491.fc37.s390x.rpm 123 kB/s | 19 kB 00:00 (29/71): perl-Exporter-5.77-489.fc37.noarch.rpm 209 kB/s | 31 kB 00:00 (30/71): perl-Fcntl-1.15-491.fc37.s390x.rpm 162 kB/s | 25 kB 00:00 (31/71): perl-File-Basename-2.85-491.fc37.noarc 146 kB/s | 22 kB 00:00 (32/71): perl-File-Path-2.18-489.fc37.noarch.rp 227 kB/s | 35 kB 00:00 (33/71): perl-File-Temp-0.231.100-489.fc37.noar 397 kB/s | 59 kB 00:00 (34/71): perl-Encode-3.19-491.fc37.s390x.rpm 2.8 MB/s | 1.7 MB 00:00 (35/71): perl-File-stat-1.12-491.fc37.noarch.rp 140 kB/s | 22 kB 00:00 (36/71): perl-FindBin-1.53-491.fc37.noarch.rpm 123 kB/s | 18 kB 00:00 (37/71): perl-Getopt-Long-2.52-489.fc37.noarch. 401 kB/s | 60 kB 00:00 (38/71): perl-Getopt-Std-1.13-491.fc37.noarch.r 131 kB/s | 20 kB 00:00 (39/71): perl-HTTP-Tiny-0.082-1.fc37.noarch.rpm 372 kB/s | 55 kB 00:00 (40/71): perl-IO-1.50-491.fc37.s390x.rpm 644 kB/s | 96 kB 00:00 (41/71): perl-IPC-Open3-1.22-491.fc37.noarch.rp 177 kB/s | 27 kB 00:00 (42/71): perl-PathTools-3.84-489.fc37.s390x.rpm 577 kB/s | 89 kB 00:00 (43/71): perl-Pod-Escapes-1.07-489.fc37.noarch. 128 kB/s | 20 kB 00:00 (44/71): perl-POSIX-2.03-491.fc37.s390x.rpm 224 kB/s | 101 kB 00:00 (45/71): perl-Pod-Perldoc-3.28.01-490.fc37.noar 581 kB/s | 90 kB 00:00 (46/71): perl-Pod-Simple-3.43-490.fc37.noarch.r 1.5 MB/s | 225 kB 00:00 (47/71): perl-Pod-Usage-2.03-3.fc37.noarch.rpm 262 kB/s | 40 kB 00:00 (48/71): perl-MIME-Base64-3.16-489.fc37.s390x.r 42 kB/s | 30 kB 00:00 (49/71): perl-Scalar-List-Utils-1.63-489.fc38.s 470 kB/s | 71 kB 00:00 (50/71): perl-SelectSaver-1.02-491.fc37.noarch. 105 kB/s | 16 kB 00:00 (51/71): perl-Socket-2.035-2.fc37.s390x.rpm 369 kB/s | 55 kB 00:00 (52/71): perl-Storable-3.26-489.fc37.s390x.rpm 622 kB/s | 93 kB 00:00 (53/71): perl-Symbol-1.09-491.fc37.noarch.rpm 121 kB/s | 19 kB 00:00 (54/71): perl-Term-ANSIColor-5.01-490.fc37.noar 323 kB/s | 48 kB 00:00 (55/71): perl-Term-Cap-1.17-489.fc37.noarch.rpm 147 kB/s | 22 kB 00:00 (56/71): perl-Text-ParseWords-3.31-489.fc37.noa 107 kB/s | 16 kB 00:00 (57/71): perl-Text-Tabs+Wrap-2021.0814-489.fc37 150 kB/s | 22 kB 00:00 (58/71): perl-Time-Local-1.300-489.fc37.noarch. 226 kB/s | 33 kB 00:00 (59/71): perl-constant-1.33-490.fc37.noarch.rpm 149 kB/s | 23 kB 00:00 (60/71): perl-if-0.61.000-491.fc37.noarch.rpm 124 kB/s | 18 kB 00:00 (61/71): perl-interpreter-5.36.0-491.fc37.s390x 514 kB/s | 76 kB 00:00 (62/71): perl-lib-0.65-491.fc37.s390x.rpm 124 kB/s | 19 kB 00:00 (63/71): perl-mro-1.26-491.fc37.s390x.rpm 221 kB/s | 33 kB 00:00 (64/71): perl-overload-1.35-491.fc37.noarch.rpm 324 kB/s | 50 kB 00:00 (65/71): perl-overloading-0.02-491.fc37.noarch. 116 kB/s | 17 kB 00:00 (66/71): perl-parent-0.238-489.fc37.noarch.rpm 91 kB/s | 14 kB 00:00 (67/71): perl-podlators-4.14-489.fc37.noarch.rp 782 kB/s | 116 kB 00:00 (68/71): perl-libs-5.36.0-491.fc37.s390x.rpm 3.7 MB/s | 2.2 MB 00:00 (69/71): perl-subs-1.04-491.fc37.noarch.rpm 105 kB/s | 16 kB 00:00 (70/71): perl-vars-1.05-491.fc37.noarch.rpm 117 kB/s | 17 kB 00:00 (71/71): zlib-devel-1.2.12-4.fc37.s390x.rpm 298 kB/s | 44 kB 00:00 -------------------------------------------------------------------------------- Total 1.9 MB/s | 53 MB 00:28 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-5.fc37.s390x 1/71 Installing : htslib-1.15.1-1.fc38.s390x 2/71 Installing : cpp-12.1.1-4.fc38.s390x 3/71 Installing : ncurses-c++-libs-6.3-3.20220501.fc37.s390x 4/71 Installing : ncurses-6.3-3.20220501.fc37.s390x 5/71 Installing : libubsan-12.1.1-4.fc38.s390x 6/71 Installing : libtool-ltdl-2.4.7-2.fc37.s390x 7/71 Installing : libatomic-12.1.1-4.fc38.s390x 8/71 Installing : libasan-12.1.1-4.fc38.s390x 9/71 Installing : kernel-headers-5.19.0-1.fc37.s390x 10/71 Running scriptlet: groff-base-1.22.4-10.fc37.s390x 11/71 Installing : groff-base-1.22.4-10.fc37.s390x 11/71 Running scriptlet: groff-base-1.22.4-10.fc37.s390x 11/71 Installing : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 12/71 Installing : perl-if-0.61.000-491.fc37.noarch 13/71 Installing : perl-Time-Local-2:1.300-489.fc37.noarch 14/71 Installing : perl-File-Path-2.18-489.fc37.noarch 15/71 Installing : perl-Pod-Escapes-1:1.07-489.fc37.noarch 16/71 Installing : perl-Class-Struct-0.66-491.fc37.noarch 17/71 Installing : perl-POSIX-2.03-491.fc37.s390x 18/71 Installing : perl-Term-ANSIColor-5.01-490.fc37.noarch 19/71 Installing : perl-IPC-Open3-1.22-491.fc37.noarch 20/71 Installing : perl-HTTP-Tiny-0.082-1.fc37.noarch 21/71 Installing : perl-subs-1.04-491.fc37.noarch 22/71 Installing : perl-File-Temp-1:0.231.100-489.fc37.noarch 23/71 Installing : perl-Term-Cap-1.17-489.fc37.noarch 24/71 Installing : perl-Pod-Simple-1:3.43-490.fc37.noarch 25/71 Installing : perl-Socket-4:2.035-2.fc37.s390x 26/71 Installing : perl-SelectSaver-1.02-491.fc37.noarch 27/71 Installing : perl-Symbol-1.09-491.fc37.noarch 28/71 Installing : perl-File-stat-1.12-491.fc37.noarch 29/71 Installing : perl-podlators-1:4.14-489.fc37.noarch 30/71 Installing : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 31/71 Installing : perl-Fcntl-1.15-491.fc37.s390x 32/71 Installing : perl-Text-ParseWords-3.31-489.fc37.noarch 33/71 Installing : perl-mro-1.26-491.fc37.s390x 34/71 Installing : perl-IO-1.50-491.fc37.s390x 35/71 Installing : perl-overloading-0.02-491.fc37.noarch 36/71 Installing : perl-Pod-Usage-4:2.03-3.fc37.noarch 37/71 Installing : perl-Errno-1.36-491.fc37.s390x 38/71 Installing : perl-File-Basename-2.85-491.fc37.noarch 39/71 Installing : perl-Getopt-Std-1.13-491.fc37.noarch 40/71 Installing : perl-MIME-Base64-3.16-489.fc37.s390x 41/71 Installing : perl-Scalar-List-Utils-5:1.63-489.fc38.s390x 42/71 Installing : perl-constant-1.33-490.fc37.noarch 43/71 Installing : perl-Storable-1:3.26-489.fc37.s390x 44/71 Installing : perl-overload-1.35-491.fc37.noarch 45/71 Installing : perl-parent-1:0.238-489.fc37.noarch 46/71 Installing : perl-vars-1.05-491.fc37.noarch 47/71 Installing : perl-Getopt-Long-1:2.52-489.fc37.noarch 48/71 Installing : perl-Carp-1.52-489.fc37.noarch 49/71 Installing : perl-Exporter-5.77-489.fc37.noarch 50/71 Installing : perl-PathTools-3.84-489.fc37.s390x 51/71 Installing : perl-DynaLoader-1.52-491.fc37.s390x 52/71 Installing : perl-Encode-4:3.19-491.fc37.s390x 53/71 Installing : perl-libs-4:5.36.0-491.fc37.s390x 54/71 Installing : perl-interpreter-4:5.36.0-491.fc37.s390x 55/71 Installing : glibc-headers-s390-2.36-1.fc37.noarch 56/71 Installing : libxcrypt-devel-4.4.28-3.fc38.s390x 57/71 Installing : glibc-devel-2.36-1.fc37.s390x 58/71 Installing : gc-8.0.6-4.fc37.s390x 59/71 Installing : guile22-2.2.7-6.fc37.s390x 60/71 Installing : make-1:4.3-11.fc37.s390x 61/71 Installing : gcc-12.1.1-4.fc38.s390x 62/71 Running scriptlet: gcc-12.1.1-4.fc38.s390x 62/71 Installing : annobin-docs-10.81-1.fc38.noarch 63/71 Installing : annobin-plugin-gcc-10.81-1.fc38.s390x 64/71 Running scriptlet: annobin-plugin-gcc-10.81-1.fc38.s390x 64/71 Installing : gcc-plugin-annobin-12.1.1-4.fc38.s390x 65/71 Installing : perl-FindBin-1.53-491.fc37.noarch 66/71 Installing : perl-lib-0.65-491.fc37.s390x 67/71 Installing : ncurses-devel-6.3-3.20220501.fc37.s390x 68/71 Installing : htslib-devel-1.15.1-1.fc38.s390x 69/71 Installing : htslib-tools-1.15.1-1.fc38.s390x 70/71 Installing : zlib-devel-1.2.12-4.fc37.s390x 71/71 Running scriptlet: zlib-devel-1.2.12-4.fc37.s390x 71/71 Verifying : htslib-1.15.1-1.fc38.s390x 1/71 Verifying : htslib-devel-1.15.1-1.fc38.s390x 2/71 Verifying : htslib-tools-1.15.1-1.fc38.s390x 3/71 Verifying : annobin-docs-10.81-1.fc38.noarch 4/71 Verifying : annobin-plugin-gcc-10.81-1.fc38.s390x 5/71 Verifying : cpp-12.1.1-4.fc38.s390x 6/71 Verifying : gc-8.0.6-4.fc37.s390x 7/71 Verifying : gcc-12.1.1-4.fc38.s390x 8/71 Verifying : gcc-plugin-annobin-12.1.1-4.fc38.s390x 9/71 Verifying : glibc-devel-2.36-1.fc37.s390x 10/71 Verifying : glibc-headers-s390-2.36-1.fc37.noarch 11/71 Verifying : groff-base-1.22.4-10.fc37.s390x 12/71 Verifying : guile22-2.2.7-6.fc37.s390x 13/71 Verifying : kernel-headers-5.19.0-1.fc37.s390x 14/71 Verifying : libasan-12.1.1-4.fc38.s390x 15/71 Verifying : libatomic-12.1.1-4.fc38.s390x 16/71 Verifying : libmpc-1.2.1-5.fc37.s390x 17/71 Verifying : libtool-ltdl-2.4.7-2.fc37.s390x 18/71 Verifying : libubsan-12.1.1-4.fc38.s390x 19/71 Verifying : libxcrypt-devel-4.4.28-3.fc38.s390x 20/71 Verifying : make-1:4.3-11.fc37.s390x 21/71 Verifying : ncurses-6.3-3.20220501.fc37.s390x 22/71 Verifying : ncurses-c++-libs-6.3-3.20220501.fc37.s390x 23/71 Verifying : ncurses-devel-6.3-3.20220501.fc37.s390x 24/71 Verifying : perl-Carp-1.52-489.fc37.noarch 25/71 Verifying : perl-Class-Struct-0.66-491.fc37.noarch 26/71 Verifying : perl-DynaLoader-1.52-491.fc37.s390x 27/71 Verifying : perl-Encode-4:3.19-491.fc37.s390x 28/71 Verifying : perl-Errno-1.36-491.fc37.s390x 29/71 Verifying : perl-Exporter-5.77-489.fc37.noarch 30/71 Verifying : perl-Fcntl-1.15-491.fc37.s390x 31/71 Verifying : perl-File-Basename-2.85-491.fc37.noarch 32/71 Verifying : perl-File-Path-2.18-489.fc37.noarch 33/71 Verifying : perl-File-Temp-1:0.231.100-489.fc37.noarch 34/71 Verifying : perl-File-stat-1.12-491.fc37.noarch 35/71 Verifying : perl-FindBin-1.53-491.fc37.noarch 36/71 Verifying : perl-Getopt-Long-1:2.52-489.fc37.noarch 37/71 Verifying : perl-Getopt-Std-1.13-491.fc37.noarch 38/71 Verifying : perl-HTTP-Tiny-0.082-1.fc37.noarch 39/71 Verifying : perl-IO-1.50-491.fc37.s390x 40/71 Verifying : perl-IPC-Open3-1.22-491.fc37.noarch 41/71 Verifying : perl-MIME-Base64-3.16-489.fc37.s390x 42/71 Verifying : perl-POSIX-2.03-491.fc37.s390x 43/71 Verifying : perl-PathTools-3.84-489.fc37.s390x 44/71 Verifying : perl-Pod-Escapes-1:1.07-489.fc37.noarch 45/71 Verifying : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 46/71 Verifying : perl-Pod-Simple-1:3.43-490.fc37.noarch 47/71 Verifying : perl-Pod-Usage-4:2.03-3.fc37.noarch 48/71 Verifying : perl-Scalar-List-Utils-5:1.63-489.fc38.s390x 49/71 Verifying : perl-SelectSaver-1.02-491.fc37.noarch 50/71 Verifying : perl-Socket-4:2.035-2.fc37.s390x 51/71 Verifying : perl-Storable-1:3.26-489.fc37.s390x 52/71 Verifying : perl-Symbol-1.09-491.fc37.noarch 53/71 Verifying : perl-Term-ANSIColor-5.01-490.fc37.noarch 54/71 Verifying : perl-Term-Cap-1.17-489.fc37.noarch 55/71 Verifying : perl-Text-ParseWords-3.31-489.fc37.noarch 56/71 Verifying : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 57/71 Verifying : perl-Time-Local-2:1.300-489.fc37.noarch 58/71 Verifying : perl-constant-1.33-490.fc37.noarch 59/71 Verifying : perl-if-0.61.000-491.fc37.noarch 60/71 Verifying : perl-interpreter-4:5.36.0-491.fc37.s390x 61/71 Verifying : perl-lib-0.65-491.fc37.s390x 62/71 Verifying : perl-libs-4:5.36.0-491.fc37.s390x 63/71 Verifying : perl-mro-1.26-491.fc37.s390x 64/71 Verifying : perl-overload-1.35-491.fc37.noarch 65/71 Verifying : perl-overloading-0.02-491.fc37.noarch 66/71 Verifying : perl-parent-1:0.238-489.fc37.noarch 67/71 Verifying : perl-podlators-1:4.14-489.fc37.noarch 68/71 Verifying : perl-subs-1.04-491.fc37.noarch 69/71 Verifying : perl-vars-1.05-491.fc37.noarch 70/71 Verifying : zlib-devel-1.2.12-4.fc37.s390x 71/71 Installed products updated. Installed: annobin-docs-10.81-1.fc38.noarch annobin-plugin-gcc-10.81-1.fc38.s390x cpp-12.1.1-4.fc38.s390x gc-8.0.6-4.fc37.s390x gcc-12.1.1-4.fc38.s390x gcc-plugin-annobin-12.1.1-4.fc38.s390x glibc-devel-2.36-1.fc37.s390x glibc-headers-s390-2.36-1.fc37.noarch groff-base-1.22.4-10.fc37.s390x guile22-2.2.7-6.fc37.s390x htslib-1.15.1-1.fc38.s390x htslib-devel-1.15.1-1.fc38.s390x htslib-tools-1.15.1-1.fc38.s390x kernel-headers-5.19.0-1.fc37.s390x libasan-12.1.1-4.fc38.s390x libatomic-12.1.1-4.fc38.s390x libmpc-1.2.1-5.fc37.s390x libtool-ltdl-2.4.7-2.fc37.s390x libubsan-12.1.1-4.fc38.s390x libxcrypt-devel-4.4.28-3.fc38.s390x make-1:4.3-11.fc37.s390x ncurses-6.3-3.20220501.fc37.s390x ncurses-c++-libs-6.3-3.20220501.fc37.s390x ncurses-devel-6.3-3.20220501.fc37.s390x perl-Carp-1.52-489.fc37.noarch perl-Class-Struct-0.66-491.fc37.noarch perl-DynaLoader-1.52-491.fc37.s390x perl-Encode-4:3.19-491.fc37.s390x perl-Errno-1.36-491.fc37.s390x perl-Exporter-5.77-489.fc37.noarch perl-Fcntl-1.15-491.fc37.s390x perl-File-Basename-2.85-491.fc37.noarch perl-File-Path-2.18-489.fc37.noarch perl-File-Temp-1:0.231.100-489.fc37.noarch perl-File-stat-1.12-491.fc37.noarch perl-FindBin-1.53-491.fc37.noarch perl-Getopt-Long-1:2.52-489.fc37.noarch perl-Getopt-Std-1.13-491.fc37.noarch perl-HTTP-Tiny-0.082-1.fc37.noarch perl-IO-1.50-491.fc37.s390x perl-IPC-Open3-1.22-491.fc37.noarch perl-MIME-Base64-3.16-489.fc37.s390x perl-POSIX-2.03-491.fc37.s390x perl-PathTools-3.84-489.fc37.s390x perl-Pod-Escapes-1:1.07-489.fc37.noarch perl-Pod-Perldoc-3.28.01-490.fc37.noarch perl-Pod-Simple-1:3.43-490.fc37.noarch perl-Pod-Usage-4:2.03-3.fc37.noarch perl-Scalar-List-Utils-5:1.63-489.fc38.s390x perl-SelectSaver-1.02-491.fc37.noarch perl-Socket-4:2.035-2.fc37.s390x perl-Storable-1:3.26-489.fc37.s390x perl-Symbol-1.09-491.fc37.noarch perl-Term-ANSIColor-5.01-490.fc37.noarch perl-Term-Cap-1.17-489.fc37.noarch perl-Text-ParseWords-3.31-489.fc37.noarch perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch perl-Time-Local-2:1.300-489.fc37.noarch perl-constant-1.33-490.fc37.noarch perl-if-0.61.000-491.fc37.noarch perl-interpreter-4:5.36.0-491.fc37.s390x perl-lib-0.65-491.fc37.s390x perl-libs-4:5.36.0-491.fc37.s390x perl-mro-1.26-491.fc37.s390x perl-overload-1.35-491.fc37.noarch perl-overloading-0.02-491.fc37.noarch perl-parent-1:0.238-489.fc37.noarch perl-podlators-1:4.14-489.fc37.noarch perl-subs-1.04-491.fc37.noarch perl-vars-1.05-491.fc37.noarch zlib-devel-1.2.12-4.fc37.s390x Complete! Finish: build setup for samtools-1.15.1-1.fc38.src.rpm Start: rpmbuild samtools-1.15.1-1.fc38.src.rpm Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1660521600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.JJ7Cut + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf samtools-1.15.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/samtools-1.15.1.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd samtools-1.15.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm -f INSTALL + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.6EGs4O + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -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 -march=zEC12 -mtune=z13 -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 -march=zEC12 -mtune=z13 -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 -march=zEC12 -mtune=z13 -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh samtools 1.15.1-1.fc38 s390x + cd samtools-1.15.1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -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 -march=zEC12 -mtune=z13 -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 -march=zEC12 -mtune=z13 -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 -march=zEC12 -mtune=z13 -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure --- ./htslib-1.15.1/configure.backup 2022-04-07 15:42:52.000000000 +0000 +++ ./htslib-1.15.1/configure 2022-08-15 14:30:47.115748022 +0000 @@ -1697,7 +1697,7 @@ #ifdef __cplusplus extern "C" #endif -char $2 (); +__attribute__ ((used)) char $2 (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh + ./configure --build=s390x-redhat-linux-gnu --host=s390x-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld' --prefix=/usr --with-htslib=system checking for gawk... gawk checking for s390x-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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for NcursesW wide-character library... yes checking for working ncursesw/curses.h... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h + /usr/bin/make -O -j2 V=1 VERBOSE=1 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_aux.o bam_aux.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam.o bam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_index.o bam_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_plcmd.o bam_plcmd.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_view.o sam_view.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_fastq.o bam_fastq.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_cat.o bam_cat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_plbuf.o bam_plbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_md.o bam_md.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_reheader.o bam_reheader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_rmdup.o bam_rmdup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_rmdupse.o bam_rmdupse.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_mate.o bam_mate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_stat.o bam_stat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.15.1"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS ""' >> version.h echo '#define SAMTOOLS_CFLAGS "-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam2bcf.o bam2bcf.c bam2bcf.c: In function 'bcf_call_glfgen': bam2bcf.c:81:33: warning: argument 2 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 81 | bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:30, from /usr/include/htslib/hts.h:37, from bam2bcf.c:30: /usr/include/stdlib.h:564:14: note: in a call to allocation function 'realloc' declared here 564 | extern void *realloc (void *__ptr, size_t __size) | ^~~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sample.o sample.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o cut_target.o cut_target.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_sort.o bam_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o phase.o phase.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam2depth.o bam2depth.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o coverage.o coverage.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o padding.o padding.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bedcov.o bedcov.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o dict.o dict.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bamshuf.o bamshuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o stats_isize.o stats_isize.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_flags.o bam_flags.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_split.o bam_split.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview.o bam_tview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o stats.o stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview_curses.o bam_tview_curses.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview_html.o bam_tview_html.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_quickcheck.o bam_quickcheck.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_lpileup.o bam_lpileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_addrprg.o bam_addrprg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o tmp_file.o tmp_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_ampliconclip.o bam_ampliconclip.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_markdup.o bam_markdup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_import.o bam_import.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_samples.o bam_samples.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o amplicon_stats.o amplicon_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o consensus_pileup.o consensus_pileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_consensus.o bam_consensus.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_opts.o sam_opts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_utils.o sam_utils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bedidx.o bedidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/ace2sam.o misc/ace2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -DMAQ_LONGREADS -I. -I./lz4 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/md5fa.o misc/md5fa.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o lz4/lz4.o lz4/lz4.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/wgsim.o misc/wgsim.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/test.o test/test.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bamtk.o bamtk.c ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld -o samtools bam.o bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz -lpthread In function 'bcf_call_glfgen', inlined from 'tv_pl_func' at bam_tview.c:196:9: bam2bcf.c:81:33: warning: argument 2 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 81 | bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); | ^ /usr/include/stdlib.h: In function 'tv_pl_func': /usr/include/stdlib.h:564:14: note: in a call to allocation function 'realloc' declared here 564 | extern void *realloc (void *__ptr, size_t __size) | ^ + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.HQGeUl + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x '!=' / ']' + rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x ++ dirname /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -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 -march=zEC12 -mtune=z13 -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 -march=zEC12 -mtune=z13 -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 -march=zEC12 -mtune=z13 -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd samtools-1.15.1 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/share/man/man1 /usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin /usr/bin/install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin /usr/bin/install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin /usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/share/man/man1 ++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/zoom2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/blast2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/bowtie2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/export2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/fasta-sanitize.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/interpolate_sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/novo2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/plot-ampliconstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/plot-bamstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/psl2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/sam2vcf.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/samtools.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/seq_cache_populate.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/soap2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/wgsim_eval.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/zoom2sam.pl + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.15.1-1.fc38 --unique-debug-suffix -1.15.1-1.fc38.s390x --unique-debug-src-base samtools-1.15.1-1.fc38.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.15.1 extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/maq2sam-long extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/ace2sam extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/maq2sam-short extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/md5fa extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/md5sum-lite extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/samtools extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/bin/wgsim original debug info size: 2112kB, size after compression: 1908kB /usr/bin/sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match. 2442 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/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.BNHsgZ + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -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 -march=zEC12 -mtune=z13 -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 -march=zEC12 -mtune=z13 -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 -march=zEC12 -mtune=z13 -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.s390x.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh samtools 1.15.1-1.fc38 s390x + cd samtools-1.15.1 + ldd samtools + grep -E '/lib(64)?/libhts\.so\.' libhts.so.3 => /lib64/libhts.so.3 (0x000003ffb6880000) + make test test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip= ${TEST_OPTS:-} bgzip -c -b 65272 -s 5 /tmp/prezAd4sDw/bgzip.dat.gz .. ok bgzip -c -b 979200 -s 6 /tmp/prezAd4sDw/bgzip.dat.gz .. ok bgzip -c -b 652804 -s 6 /tmp/prezAd4sDw/bgzip.dat.gz .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/prezAd4sDw/faidx.fa 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/prezAd4sDw/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/prezAd4sDw/faidx.fa 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/prezAd4sDw/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/prezAd4sDw/faidx.fa 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/prezAd4sDw/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/prezAd4sDw/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/prezAd4sDw/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/prezAd4sDw/fqidx.fq 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/prezAd4sDw/fqidx.fq.gz 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/prezAd4sDw/fqidx.fq 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/prezAd4sDw/fqidx.fq.gz 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/prezAd4sDw/fqidx.fq 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/prezAd4sDw/fqidx.fq.gz 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/prezAd4sDw/fqidx.fq 1:99998-100007 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/prezAd4sDw/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /builddir/build/BUILD/samtools-1.15.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /builddir/build/BUILD/samtools-1.15.1/test/dat/dict.fa .. ok test_dict: /builddir/build/BUILD/samtools-1.15.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/prezAd4sDw/dict.fa.gz .. ok test_dict: cat /builddir/build/BUILD/samtools-1.15.1/test/dat/dict.fa | /builddir/build/BUILD/samtools-1.15.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /builddir/build/BUILD/samtools-1.15.1/samtools dict -AH < /builddir/build/BUILD/samtools-1.15.1/test/dat/dict.alias.fa .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view /tmp/prezAd4sDw/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view /tmp/prezAd4sDw/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view -X /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /tmp/prezAd4sDw/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools merge -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai /tmp/prezAd4sDw/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.bam /tmp/prezAd4sDw/auto_indexed.csi && cat /tmp/prezAd4sDw/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.cram /tmp/prezAd4sDw/auto_indexed.crai && cat /tmp/prezAd4sDw/auto_indexed.crai .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.sam /tmp/prezAd4sDw/auto_indexed.csi && cat /tmp/prezAd4sDw/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/prezAd4sDw/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/prezAd4sDw/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /tmp/prezAd4sDw/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai /tmp/prezAd4sDw/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.bam /tmp/prezAd4sDw/auto_indexed.csi && cat /tmp/prezAd4sDw/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.cram /tmp/prezAd4sDw/auto_indexed.crai && cat /tmp/prezAd4sDw/auto_indexed.crai .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.sam /tmp/prezAd4sDw/auto_indexed.csi && cat /tmp/prezAd4sDw/auto_indexed.csi .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/prezAd4sDw/mpileup.bam.list -f /tmp/prezAd4sDw/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/prezAd4sDw/mpileup.cram.list -f /tmp/prezAd4sDw/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/prezAd4sDw/mpileup.bam.urllist -f /tmp/prezAd4sDw/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/prezAd4sDw/mpileup.cram.urllist -f /tmp/prezAd4sDw/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/prezAd4sDw/mpileup.ref.fa.gz -r17:1050-1060 /tmp/prezAd4sDw/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/prezAd4sDw/mpileup.ref.fa.gz -r17:1050-1060 /tmp/prezAd4sDw/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup /builddir/build/BUILD/samtools-1.15.1/test/mpileup/overlap.bam | grep 128814202 test/test.pl: no IO::Pty module or can't open pty; skipping usage tests .. ok test_usage: samtools test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/prezAd4sDw/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/prezAd4sDw/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/prezAd4sDw/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/prezAd4sDw/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/prezAd4sDw/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/prezAd4sDw/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/prezAd4sDw/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/prezAd4sDw/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/prezAd4sDw/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/prezAd4sDw/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/prezAd4sDw/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/prezAd4sDw/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/prezAd4sDw/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/prezAd4sDw/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/prezAd4sDw/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/prezAd4sDw/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/prezAd4sDw/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/prezAd4sDw/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/prezAd4sDw/view.001.forn (SAM input) .. ok 68: Count -N /tmp/prezAd4sDw/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/prezAd4sDw/view.001.forn (BAM input) .. ok 70: Count -N /tmp/prezAd4sDw/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/prezAd4sDw/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/prezAd4sDw/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok 74: Count -d BC (SAM input) .. ok 75: Filter -d BC (BAM input) .. ok 76: Count -d BC (BAM input) .. ok 77: Filter -d BC (CRAM input) .. ok 78: Count -d BC (CRAM input) .. ok 79: Filter -d BC:TGCA (SAM input) .. ok 80: Count -d BC:TGCA (SAM input) .. ok 81: Filter -d BC:TGCA (BAM input) .. ok 82: Count -d BC:TGCA (BAM input) .. ok 83: Filter -d BC:TGCA (CRAM input) .. ok 84: Count -d BC:TGCA (CRAM input) .. ok 85: Filter -D BC:/tmp/prezAd4sDw/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/prezAd4sDw/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/prezAd4sDw/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/prezAd4sDw/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/prezAd4sDw/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/prezAd4sDw/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/prezAd4sDw/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/prezAd4sDw/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/prezAd4sDw/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/prezAd4sDw/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/prezAd4sDw/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/prezAd4sDw/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/prezAd4sDw/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/prezAd4sDw/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/prezAd4sDw/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/prezAd4sDw/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/prezAd4sDw/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/prezAd4sDw/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/prezAd4sDw/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/prezAd4sDw/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/prezAd4sDw/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/prezAd4sDw/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/prezAd4sDw/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/prezAd4sDw/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok 110: Count -d NE:TGCA (SAM input) .. ok 111: Filter -d NE:TGCA (BAM input) .. ok 112: Count -d NE:TGCA (BAM input) .. ok 113: Filter -d NE:TGCA (CRAM input) .. ok 114: Count -d NE:TGCA (CRAM input) .. ok 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/prezAd4sDw/view.test115.sam -h -d TGCA /tmp/prezAd4sDw/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -d TGCA /tmp/prezAd4sDw/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/prezAd4sDw/view.test117.sam -h -d TGCA /tmp/prezAd4sDw/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -d TGCA /tmp/prezAd4sDw/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/prezAd4sDw/view.test119.sam -h -d TGCA /tmp/prezAd4sDw/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -d TGCA /tmp/prezAd4sDw/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/prezAd4sDw/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/prezAd4sDw/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/prezAd4sDw/view.test121.sam -h -D BClong:/tmp/prezAd4sDw/view.001.fobc /tmp/prezAd4sDw/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/prezAd4sDw/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/prezAd4sDw/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/prezAd4sDw/view.001.fobc /tmp/prezAd4sDw/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/prezAd4sDw/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/prezAd4sDw/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/prezAd4sDw/view.test123.sam -h -D BClong:/tmp/prezAd4sDw/view.001.fobc /tmp/prezAd4sDw/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/prezAd4sDw/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/prezAd4sDw/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/prezAd4sDw/view.001.fobc /tmp/prezAd4sDw/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/prezAd4sDw/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/prezAd4sDw/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/prezAd4sDw/view.test125.sam -h -D BClong:/tmp/prezAd4sDw/view.001.fobc /tmp/prezAd4sDw/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/prezAd4sDw/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/prezAd4sDw/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/prezAd4sDw/view.001.fobc /tmp/prezAd4sDw/view.test006.cram --no-PG .. expected failure 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/prezAd4sDw/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/prezAd4sDw/view.001.sam --no-PG .. expected failure 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/prezAd4sDw/view.001.sam --no-PG .. expected failure 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/prezAd4sDw/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/prezAd4sDw/view.test001.bam --no-PG .. expected failure 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/prezAd4sDw/view.test001.bam --no-PG .. expected failure 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/prezAd4sDw/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/prezAd4sDw/view.test006.cram --no-PG .. expected failure 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/prezAd4sDw/view.test006.cram --no-PG .. expected failure 133: Filter -d NM:13 (SAM input) .. ok 134: Count -d NM:13 (SAM input) .. ok 135: Filter -d NM:13 (BAM input) .. ok 136: Count -d NM:13 (BAM input) .. ok 137: Filter -d NM:13 (CRAM input) .. ok 138: Count -d NM:13 (CRAM input) .. ok 139: Filter -d ab:z (SAM input) .. ok 140: Count -d ab:z (SAM input) .. ok 141: Filter -d ab:z (BAM input) .. ok 142: Count -d ab:z (BAM input) .. ok 143: Filter -d ab:z (CRAM input) .. ok 144: Count -d ab:z (CRAM input) .. ok 145: Filter -l Library 2 (SAM input) .. ok 146: Count -l Library 2 (SAM input) .. ok 147: Filter -l Library 2 (BAM input) .. ok 148: Count -l Library 2 (BAM input) .. ok 149: Filter -l Library 2 (CRAM input) .. ok 150: Count -l Library 2 (CRAM input) .. ok 151: Filter -l Library 3 (SAM input) .. ok 152: Count -l Library 3 (SAM input) .. ok 153: Filter -l Library 3 (BAM input) .. ok 154: Count -l Library 3 (BAM input) .. ok 155: Filter -l Library 3 (CRAM input) .. ok 156: Count -l Library 3 (CRAM input) .. ok 157: Filter -q 50 (SAM input) .. ok 158: Count -q 50 (SAM input) .. ok 159: Filter -q 50 (BAM input) .. ok 160: Count -q 50 (BAM input) .. ok 161: Filter -q 50 (CRAM input) .. ok 162: Count -q 50 (CRAM input) .. ok 163: Filter -q 99 (SAM input) .. ok 164: Count -q 99 (SAM input) .. ok 165: Filter -q 99 (BAM input) .. ok 166: Count -q 99 (BAM input) .. ok 167: Filter -q 99 (CRAM input) .. ok 168: Count -q 99 (CRAM input) .. ok 169: Filter -q 100 (SAM input) .. ok 170: Count -q 100 (SAM input) .. ok 171: Filter -q 100 (BAM input) .. ok 172: Count -q 100 (BAM input) .. ok 173: Filter -q 100 (CRAM input) .. ok 174: Count -q 100 (CRAM input) .. ok 175: Filter -x fa (SAM input) .. ok 176: Count -x fa (SAM input) .. ok 177: Filter -x fa (BAM input) .. ok 178: Count -x fa (BAM input) .. ok 179: Filter -x fa (CRAM input) .. ok 180: Count -x fa (CRAM input) .. ok 181: Filter -x fa -x ha (SAM input) .. ok 182: Count -x fa -x ha (SAM input) .. ok 183: Filter -x fa -x ha (BAM input) .. ok 184: Count -x fa -x ha (BAM input) .. ok 185: Filter -x fa -x ha (CRAM input) .. ok 186: Count -x fa -x ha (CRAM input) .. ok 187: Filter -x fa,ha (SAM input) .. ok 188: Count -x fa,ha (SAM input) .. ok 189: Filter -x fa,ha (BAM input) .. ok 190: Count -x fa,ha (BAM input) .. ok 191: Filter -x fa,ha (CRAM input) .. ok 192: Count -x fa,ha (CRAM input) .. ok 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 205: Filter -x fa -r grp2 (SAM input) .. ok 206: Count -x fa -r grp2 (SAM input) .. ok 207: Filter -x fa -r grp2 (BAM input) .. ok 208: Count -x fa -r grp2 (BAM input) .. ok 209: Filter -x fa -r grp2 (CRAM input) .. ok 210: Count -x fa -r grp2 (CRAM input) .. ok 211: Filter -x RG -r grp2 (SAM input) .. ok 212: Count -x RG -r grp2 (SAM input) .. ok 213: Filter -x RG -r grp2 (BAM input) .. ok 214: Count -x RG -r grp2 (BAM input) .. ok 215: Filter -x RG -r grp2 (CRAM input) .. ok 216: Count -x RG -r grp2 (CRAM input) .. ok 217: Filter -m 10 (SAM input) .. ok 218: Count -m 10 (SAM input) .. ok 219: Filter -m 10 (BAM input) .. ok 220: Count -m 10 (BAM input) .. ok 221: Filter -m 10 (CRAM input) .. ok 222: Count -m 10 (CRAM input) .. ok 223: Filter -m 11 (SAM input) .. ok 224: Count -m 11 (SAM input) .. ok 225: Filter -m 11 (BAM input) .. ok 226: Count -m 11 (BAM input) .. ok 227: Filter -m 11 (CRAM input) .. ok 228: Count -m 11 (CRAM input) .. ok 229: Filter -m 15 (SAM input) .. ok 230: Count -m 15 (SAM input) .. ok 231: Filter -m 15 (BAM input) .. ok 232: Count -m 15 (BAM input) .. ok 233: Filter -m 15 (CRAM input) .. ok 234: Count -m 15 (CRAM input) .. ok 235: Filter -m 16 (SAM input) .. ok 236: Count -m 16 (SAM input) .. ok 237: Filter -m 16 (BAM input) .. ok 238: Count -m 16 (BAM input) .. ok 239: Filter -m 16 (CRAM input) .. ok 240: Count -m 16 (CRAM input) .. ok 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 247: Filter -e [BC] (SAM input) .. ok 248: Count -e [BC] (SAM input) .. ok 249: Filter -e [BC] (BAM input) .. ok 250: Count -e [BC] (BAM input) .. ok 251: Filter -e [BC] (CRAM input) .. ok 252: Count -e [BC] (CRAM input) .. ok 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 259: Filter -e mapq >= 50 (SAM input) .. ok 260: Count -e mapq >= 50 (SAM input) .. ok 261: Filter -e mapq >= 50 (BAM input) .. ok 262: Count -e mapq >= 50 (BAM input) .. ok 263: Filter -e mapq >= 50 (CRAM input) .. ok 264: Count -e mapq >= 50 (CRAM input) .. ok 265: Filter -e mapq >= 99 (SAM input) .. ok 266: Count -e mapq >= 99 (SAM input) .. ok 267: Filter -e mapq >= 99 (BAM input) .. ok 268: Count -e mapq >= 99 (BAM input) .. ok 269: Filter -e mapq >= 99 (CRAM input) .. ok 270: Count -e mapq >= 99 (CRAM input) .. ok 271: Filter -e mapq >= 100 (SAM input) .. ok 272: Count -e mapq >= 100 (SAM input) .. ok 273: Filter -e mapq >= 100 (BAM input) .. ok 274: Count -e mapq >= 100 (BAM input) .. ok 275: Filter -e mapq >= 100 (CRAM input) .. ok 276: Count -e mapq >= 100 (CRAM input) .. ok 277: 1bp reads file SAM -> BAM -> SAM .. ok 278: 1bp reads file SAM -> CRAM -> SAM .. ok 278: Region Z (BAM input) .. ok 279: Count Z (BAM input) .. ok 280: Region Z (CRAM input) .. ok 281: Count Z (CRAM input) .. ok 282: Region Z:30 (BAM input) .. ok 283: Count Z:30 (BAM input) .. ok 284: Region Z:30 (CRAM input) .. ok 285: Count Z:30 (CRAM input) .. ok 286: Region Z:20-40 (BAM input) .. ok 287: Count Z:20-40 (BAM input) .. ok 288: Region Z:20-40 (CRAM input) .. ok 289: Count Z:20-40 (CRAM input) .. ok 290: Region ref1 (BAM input) .. ok 291: Count ref1 (BAM input) .. ok 292: Region ref1 (CRAM input) .. ok 293: Count ref1 (CRAM input) .. ok 294: Region ref1:15 (BAM input) .. ok 295: Count ref1:15 (BAM input) .. ok 296: Region ref1:15 (CRAM input) .. ok 297: Count ref1:15 (CRAM input) .. ok 298: Region ref1:15-45 (BAM input) .. ok 299: Count ref1:15-45 (BAM input) .. ok 300: Region ref1:15-45 (CRAM input) .. ok 301: Count ref1:15-45 (CRAM input) .. ok 302: Region ref1:15-45 ref2 (BAM input) .. ok 303: Count ref1:15-45 ref2 (BAM input) .. ok 304: Region ref1:15-45 ref2 (CRAM input) .. ok 305: Count ref1:15-45 ref2 (CRAM input) .. ok 306: Region ref1:15-45 ref2:16 (BAM input) .. ok 307: Count ref1:15-45 ref2:16 (BAM input) .. ok 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 318: Region -f 128 ref1 (BAM input) .. ok 319: Count -f 128 ref1 (BAM input) .. ok 320: Region -f 128 ref1 (CRAM input) .. ok 321: Count -f 128 ref1 (CRAM input) .. ok 322: Region -q 50 ref1:15-45 (BAM input) .. ok 323: Count -q 50 ref1:15-45 (BAM input) .. ok 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 326: Region -r grp2 ref1:15-45 (BAM input) .. ok 327: Count -r grp2 ref1:15-45 (BAM input) .. ok 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok 330: Region * (BAM input) .. ok 331: Count * (BAM input) .. ok 332: Region * (CRAM input) .. ok 333: Count * (CRAM input) .. ok 334: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z (BAM input).. ok 351: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z (BAM input).. ok 352: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z (CRAM input).. ok 353: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z (CRAM input).. ok 354: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok 355: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok 356: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 357: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 358: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 359: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 360: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 361: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 362: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 363: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 364: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 365: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 366: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 367: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 368: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 369: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 370: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (BAM input).. ok 371: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (BAM input).. ok 372: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok 373: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok 374: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 375: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 376: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 377: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 378: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 379: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 380: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 381: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 382: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok 383: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok 384: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 385: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 386: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok 387: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok 388: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 389: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 390: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 391: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 392: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 393: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 394: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 395: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 396: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 397: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 398: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 399: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 400: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 401: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 402: Make BAM with no M5/UR tags .. ok 403: Add @SQ with -t (SAM -> SAM) .. ok 404: Add @SQ with -T (SAM -> SAM) .. ok 405: Add @SQ with -t (BAM -> SAM) .. ok 406: Add @SQ with -T (BAM -> SAM) .. ok 407: Add @SQ with -t (SAM -> BAM) .. ok 408: Add @SQ with -T (SAM -> BAM) .. ok 409: Add @SQ with -t (BAM -> BAM) .. ok 410: Add @SQ with -T (BAM -> BAM) .. ok 411: Add @SQ with -t (SAM -> CRAM) .. ok 412: Add @SQ with -T (SAM -> CRAM) .. ok 413: Add @SQ with -t (BAM -> CRAM) .. ok 414: Add @SQ with -T (BAM -> CRAM) .. ok 415: Make CRAM with no UR field .. ok 416: Decoding CRAM with no UR field via -T .. ok 417: CIGAR B-operator removal .. ok 418: Big SAM -> BAM .. ok 419: Big SAM -> BAM (2 threads) .. ok 420: Big SAM -> BAM (4 threads) .. ok 421: Big SAM -> CRAM .. ok 422: Big SAM -> CRAM (2 threads) .. ok 423: Big SAM -> CRAM (4 threads) .. ok 424: Subsample 0.2 (SAM input) ............ ok 425: Subsample 0.5 (SAM input) ............ ok 426: Subsample 0.8 (SAM input) ............ ok 427: Subsample 0.2 (BAM input) ............ ok 428: Subsample 0.5 (BAM input) ............ ok 429: Subsample 0.8 (BAM input) ............ ok 430: Subsample 0.2 (CRAM input) ............ ok 431: Subsample 0.5 (CRAM input) ............ ok 432: Subsample 0.8 (CRAM input) ............ ok 433: SAM add PG .. ok 434: Unset dup flag, remove dt and do tags .. ok 435: Unmap dup flagged reads. .. ok 436: Unmap dup flagged reads. .. ok 437: fetch pairs .. ok 438: fetch pairs .. ok 439: fetch pairs .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -h 0 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -h 1 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -h 5 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -h 29 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -h 30 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -n 0 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -n 1 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -n 5 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -h 5 -n 5 < /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import -0 test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import -s test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import -s test/bam2fq/5.s.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -T RG,BC,QT -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -T RG,BC,QT,MD,ia -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/import/2.interleaved.fq -T "" .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/import/3.interleaved.fq -i .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/import/4.aux.fq -T "*" .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/import/4.aux.fq -T "" .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ .. ok test_bam2fq: Generate BAM file .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -t -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.703.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.15.1/test/o.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fasta -N -1 /builddir/build/BUILD/samtools-1.15.1/test/o.fa -2 /builddir/build/BUILD/samtools-1.15.1/test/o.fa /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -o /builddir/build/BUILD/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -s /tmp/prezAd4sDw/bam2fq.discard.s.fq -0 /tmp/prezAd4sDw/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.013.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.15.1/test/i2.fq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.014.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -t -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.703.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -1 /builddir/build/BUILD/samtools-1.15.1/test/o.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fasta -@ 2 -N -1 /builddir/build/BUILD/samtools-1.15.1/test/o.fa -2 /builddir/build/BUILD/samtools-1.15.1/test/o.fa /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -o /builddir/build/BUILD/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -s /tmp/prezAd4sDw/bam2fq.discard.s.fq -0 /tmp/prezAd4sDw/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.013.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.15.1/test/i2.fq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.014.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa -i 0 /builddir/build/BUILD/samtools-1.15.1/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -t /builddir/build/BUILD/samtools-1.15.1/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -g 4 -t /builddir/build/BUILD/samtools-1.15.1/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -g 4 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.15.1/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.15.1/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.15.1/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.15.1/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /builddir/build/BUILD/samtools-1.15.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /builddir/build/BUILD/samtools-1.15.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /builddir/build/BUILD/samtools-1.15.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -I s1 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -I grp2 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -I grp3 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -I Sample /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam | tail -n+4 .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam -b /tmp/v4lBxw2qV5 - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/prezAd4sDw/merge.tag.1.bam /tmp/prezAd4sDw/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/prezAd4sDw/merge.tag.3.bam /tmp/prezAd4sDw/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge --no-PG -O SAM - /builddir/build/BUILD/samtools-1.15.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.15.1/test/merge/merge.bed - /tmp/prezAd4sDw/merge.bed.1.bam /tmp/prezAd4sDw/merge.bed.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/pl0xWyWZMh - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/prezAd4sDw/merge.tag.1.bam /tmp/prezAd4sDw/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/prezAd4sDw/merge.tag.3.bam /tmp/prezAd4sDw/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 --no-PG -O SAM - /builddir/build/BUILD/samtools-1.15.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.15.1/test/merge/merge.bed - /tmp/prezAd4sDw/merge.bed.1.bam /tmp/prezAd4sDw/merge.bed.2.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/prezAd4sDw/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -f /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/prezAd4sDw/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -o /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/prezAd4sDw/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -n -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -t AS -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -t FI -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/prezAd4sDw/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/prezAd4sDw/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/prezAd4sDw/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -n -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -t AS -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -t FI -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate --output-fmt=sam -O /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -o /builddir/build/BUILD/samtools-1.15.1/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -o /builddir/build/BUILD/samtools-1.15.1/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate --output-fmt=sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate --output-fmt=sam -f /builddir/build/BUILD/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam -O /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.15.1/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.15.1/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam -f /builddir/build/BUILD/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/8_isize_overflow_64bit.sam - .. ok /builddir/build/BUILD/samtools-1.15.1/samtools calmd -uAr /builddir/build/BUILD/samtools-1.15.1/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/mpileup.ref.fa .. ok /builddir/build/BUILD/samtools-1.15.1/samtools calmd -@ 2 -uAr /builddir/build/BUILD/samtools-1.15.1/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/mpileup.ref.fa .. ok test_idxstat: /builddir/build/BUILD/samtools-1.15.1/samtools idxstats /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam .. ok test_idxstat: /builddir/build/BUILD/samtools-1.15.1/samtools idxstats /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.cram .. ok test_idxstat: /builddir/build/BUILD/samtools-1.15.1/samtools idxstats /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck -v /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/1.quickcheck.badeof.bam /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/2.quickcheck.badheader.bam /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/3.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/4.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/6.quickcheck.cram21.ok.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/7.quickcheck.cram30.ok.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/8.quickcheck.cram21.truncated.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/9.quickcheck.cram30.truncated.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck -uv /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v21.cram | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader --in-place /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v21.cram && /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader --in-place /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v30.cram && /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -m orphan_only /builddir/build/BUILD/samtools-1.15.1/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -R '1#9' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -m orphan_only /builddir/build/BUILD/samtools-1.15.1/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -R '1#9' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam -r --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/8_optical_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam -r --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/8_optical_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/12_optical_chain_regex.sam - .. ok test_bedcov: /builddir/build/BUILD/samtools-1.15.1/samtools bedcov /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.15.1/samtools bedcov -j /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.15.1/samtools bedcov -g512 -G2048 /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bam .. ok test_split: /builddir/build/BUILD/samtools-1.15.1/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.15.1/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.15.1/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.15.1/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.15.1/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.15.1/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.15.1/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.15.1/test/split/split.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /tmp/prezAd4sDw/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /tmp/prezAd4sDw/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG -L /builddir/build/BUILD/samtools-1.15.1/test/large_pos/test.bed /tmp/prezAd4sDw/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools sort -O sam --no-PG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref_name.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools merge -O sam --no-PG - /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref.sam /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref2.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools depth /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools depth -b /builddir/build/BUILD/samtools-1.15.1/test/large_pos/test.bed /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/prezAd4sDw/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam --no-PG - - | /builddir/build/BUILD/samtools-1.15.1/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_hard_clipped.expected.sam /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_soft_clipped.expected.sam /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_soft_clipped_strand.expected.sam /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/2_both_clipped.expected.sam | egrep -v 'Samtools version|Command line' .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconstats/mixed_clipped.sam | egrep -v 'Samtools version|Command line' .. ok Number of tests: total .. 807 passed .. 776 failed .. 0 expected failure .. 31 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="gawk" ../regression.sh mpileup.reg === Testing mpileup.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 118 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="gawk" ../regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 47 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/consensus && AWK="gawk" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 62 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS + RPM_EC=0 ++ jobs -p + exit 0 Processing files: samtools-1.15.1-1.fc38.s390x Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.qePa32 + umask 022 + cd /builddir/build/BUILD + cd samtools-1.15.1 + DOCDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/share/doc/samtools + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/share/doc/samtools + cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/share/doc/samtools + cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/share/doc/samtools + cp -pr NEWS /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/share/doc/samtools + cp -pr examples/ /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/share/doc/samtools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.MPejft + umask 022 + cd /builddir/build/BUILD + cd samtools-1.15.1 + LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/share/licenses/samtools + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/share/licenses/samtools + cp -pr LICENSE /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x/usr/share/licenses/samtools + RPM_EC=0 ++ jobs -p + exit 0 Provides: samtools = 1.15.1-1.fc38 samtools(s390-64) = 1.15.1-1.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl libc.so.6()(64bit) libc.so.6(GLIBC_2.2)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: samtools-debugsource-1.15.1-1.fc38.s390x Provides: samtools-debugsource = 1.15.1-1.fc38 samtools-debugsource(s390-64) = 1.15.1-1.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: samtools-debuginfo-1.15.1-1.fc38.s390x Provides: debuginfo(build-id) = 1ce2ff9ea5439318fcb82ebf0aeba7d824df176e debuginfo(build-id) = 4a1706d39545603efde867158edeae424964146c debuginfo(build-id) = 689b46e1c8561abbbd9b1af34f0d782dc29cd951 debuginfo(build-id) = a6e7aa4a3840c53334cd3f8b78a7f106ce1567ac debuginfo(build-id) = ab48bf839ff2a4db6f9e4e75155b7d31b9208834 debuginfo(build-id) = bf0876de668045459ea97404db5c91407de1efcc debuginfo(build-id) = d52972c999492af24230dac54b4dae227ed1cabb samtools-debuginfo = 1.15.1-1.fc38 samtools-debuginfo(s390-64) = 1.15.1-1.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: samtools-debugsource(s390-64) = 1.15.1-1.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x Wrote: /builddir/build/RPMS/samtools-1.15.1-1.fc38.s390x.rpm Wrote: /builddir/build/RPMS/samtools-debuginfo-1.15.1-1.fc38.s390x.rpm Wrote: /builddir/build/RPMS/samtools-debugsource-1.15.1-1.fc38.s390x.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.aTJPOx + umask 022 + cd /builddir/build/BUILD + cd samtools-1.15.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.s390x + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.IO5zkU + umask 022 + cd /builddir/build/BUILD + rm -rf samtools-1.15.1 samtools-1.15.1.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild samtools-1.15.1-1.fc38.src.rpm Finish: build phase for samtools-1.15.1-1.fc38.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-s390x-1660573664.597255/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-s390x-1660573664.597255/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-s390x-1660573664.597255/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/samtools-1.15.1-1.fc38.src.rpm) Config(child) 2 minutes 32 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