Warning: Permanently added '34.229.117.115' (ED25519) to the list of known hosts.

You can reproduce this build on your computer by running:

  sudo dnf install copr-rpmbuild
  /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/6868888-amazonlinux-2023-aarch64 --chroot amazonlinux-2023-aarch64


Version: 0.70
PID: 23507
Logging PID: 23508
Task:
{'appstream': False,
 'background': False,
 'build_id': 6868888,
 'buildroot_pkgs': [],
 'chroot': 'amazonlinux-2023-aarch64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '0392ffcf610a37f721b5e82445dac25a42cacab3',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/trawets/random-al2023-pkg-builds/samtools',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'samtools',
 'package_version': '1.15.1-3',
 'project_dirname': 'random-al2023-pkg-builds',
 'project_name': 'random-al2023-pkg-builds',
 'project_owner': 'trawets',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/trawets/random-al2023-pkg-builds/amazonlinux-2023-aarch64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'trawets/random-al2023-pkg-builds--trawets',
 'source_json': {},
 'source_type': None,
 'submitter': 'trawets',
 'tags': [],
 'task_id': '6868888-amazonlinux-2023-aarch64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/trawets/random-al2023-pkg-builds/samtools /var/lib/copr-rpmbuild/workspace/workdir-0k4aumou/samtools --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/trawets/random-al2023-pkg-builds/samtools', '/var/lib/copr-rpmbuild/workspace/workdir-0k4aumou/samtools', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-0k4aumou/samtools'...

Running: git checkout 0392ffcf610a37f721b5e82445dac25a42cacab3 --

cmd: ['git', 'checkout', '0392ffcf610a37f721b5e82445dac25a42cacab3', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-0k4aumou/samtools
rc: 0
stdout: 
stderr: Note: switching to '0392ffcf610a37f721b5e82445dac25a42cacab3'.

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

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

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

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

HEAD is now at 0392ffc automatic import of samtools

Running: copr-distgit-client sources

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-0k4aumou/samtools
rc: 0
stdout: 
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading samtools-1.15.1.tar.bz2
INFO: Reading stdout from command: curl --help all
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
INFO: Calling: curl -H Pragma: -o samtools-1.15.1.tar.bz2 --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/trawets/random-al2023-pkg-builds/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   120M      0 --:--:-- --:--:-- --:--:--  122M
INFO: Reading stdout from command: md5sum samtools-1.15.1.tar.bz2

Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-0k4aumou/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-0k4aumou/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1704591447.273799 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.4 starting (python version = 3.11.3, NVR = mock-5.4-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-0k4aumou/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-0k4aumou/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1704591447.273799 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-0k4aumou/samtools/samtools.spec)  Config(amazonlinux-2023-aarch64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.4
INFO: Mock Version: 5.4
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-aarch64-bootstrap-1704591447.273799/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using bootstrap image: public.ecr.aws/amazonlinux/amazonlinux:2023
INFO: Pulling image: public.ecr.aws/amazonlinux/amazonlinux:2023
INFO: Copy content of container public.ecr.aws/amazonlinux/amazonlinux:2023 to /var/lib/mock/amazonlinux-2023-aarch64-bootstrap-1704591447.273799/root
INFO: Checking that public.ecr.aws/amazonlinux/amazonlinux:2023 image matches host's architecture
INFO: mounting public.ecr.aws/amazonlinux/amazonlinux:2023 with podman image mount
INFO: image public.ecr.aws/amazonlinux/amazonlinux:2023 as /var/lib/containers/storage/overlay/90b47655dc28817c48ff86404223b17287409bc6bb899cd0b28e2b0c754404da/merged
INFO: umounting image public.ecr.aws/amazonlinux/amazonlinux:2023 (/var/lib/containers/storage/overlay/90b47655dc28817c48ff86404223b17287409bc6bb899cd0b28e2b0c754404da/merged) with podman image umount
INFO: Package manager dnf detected and used (fallback)
INFO: Bootstrap image not marked ready
Start(bootstrap): installing dnf tooling
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                 2.1 MB/s | 172 kB     00:00    
Amazon Linux 2023 repository - aarch64           43 MB/s |  22 MB     00:00    
Package python3-dnf-4.12.0-2.amzn2023.0.4.noarch is already installed.
Dependencies resolved.
================================================================================
 Package                  Arch    Version                     Repository   Size
================================================================================
Installing:
 python3-dnf-plugins-core noarch  4.1.0-1.amzn2023.0.3        amazonlinux 219 k
Installing dependencies:
 dbus-libs                aarch64 1:1.12.28-1.amzn2023.0.1    amazonlinux 152 k
 python3-dateutil         noarch  1:2.8.1-3.amzn2023.0.2      amazonlinux 289 k
 python3-dbus             aarch64 1.2.18-1.amzn2023.0.2       amazonlinux 134 k
 python3-distro           noarch  1.5.0-5.amzn2023.0.2        amazonlinux  36 k
 python3-setuptools       noarch  59.6.0-2.amzn2023.0.4       amazonlinux 940 k
 python3-six              noarch  1.15.0-5.amzn2023.0.2       amazonlinux  36 k
 systemd-libs             aarch64 252.16-1.amzn2023.0.1       amazonlinux 597 k

Transaction Summary
================================================================================
Install  8 Packages

Total download size: 2.3 M
Installed size: 11 M
Downloading Packages:
(1/8): python3-six-1.15.0-5.amzn2023.0.2.noarch 984 kB/s |  36 kB     00:00    
(2/8): python3-dateutil-2.8.1-3.amzn2023.0.2.no 6.9 MB/s | 289 kB     00:00    
(3/8): python3-distro-1.5.0-5.amzn2023.0.2.noar 5.1 MB/s |  36 kB     00:00    
(4/8): python3-setuptools-59.6.0-2.amzn2023.0.4  20 MB/s | 940 kB     00:00    
(5/8): python3-dnf-plugins-core-4.1.0-1.amzn202  25 MB/s | 219 kB     00:00    
(6/8): dbus-libs-1.12.28-1.amzn2023.0.1.aarch64  19 MB/s | 152 kB     00:00    
(7/8): systemd-libs-252.16-1.amzn2023.0.1.aarch  53 MB/s | 597 kB     00:00    
(8/8): python3-dbus-1.2.18-1.amzn2023.0.2.aarch  10 MB/s | 134 kB     00:00    
--------------------------------------------------------------------------------
Total                                           6.3 MB/s | 2.3 MB     00:00     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Installing       : systemd-libs-252.16-1.amzn2023.0.1.aarch64             1/8 
  Installing       : dbus-libs-1:1.12.28-1.amzn2023.0.1.aarch64             2/8 
  Installing       : python3-dbus-1.2.18-1.amzn2023.0.2.aarch64             3/8 
  Installing       : python3-setuptools-59.6.0-2.amzn2023.0.4.noarch        4/8 
  Installing       : python3-distro-1.5.0-5.amzn2023.0.2.noarch             5/8 
  Installing       : python3-six-1.15.0-5.amzn2023.0.2.noarch               6/8 
  Installing       : python3-dateutil-1:2.8.1-3.amzn2023.0.2.noarch         7/8 
  Installing       : python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch   8/8 
  Running scriptlet: python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch   8/8 
  Verifying        : python3-six-1.15.0-5.amzn2023.0.2.noarch               1/8 
  Verifying        : python3-dateutil-1:2.8.1-3.amzn2023.0.2.noarch         2/8 
  Verifying        : python3-setuptools-59.6.0-2.amzn2023.0.4.noarch        3/8 
  Verifying        : python3-distro-1.5.0-5.amzn2023.0.2.noarch             4/8 
  Verifying        : python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch   5/8 
  Verifying        : systemd-libs-252.16-1.amzn2023.0.1.aarch64             6/8 
  Verifying        : dbus-libs-1:1.12.28-1.amzn2023.0.1.aarch64             7/8 
  Verifying        : python3-dbus-1.2.18-1.amzn2023.0.2.aarch64             8/8 

Installed:
  dbus-libs-1:1.12.28-1.amzn2023.0.1.aarch64                                    
  python3-dateutil-1:2.8.1-3.amzn2023.0.2.noarch                                
  python3-dbus-1.2.18-1.amzn2023.0.2.aarch64                                    
  python3-distro-1.5.0-5.amzn2023.0.2.noarch                                    
  python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch                          
  python3-setuptools-59.6.0-2.amzn2023.0.4.noarch                               
  python3-six-1.15.0-5.amzn2023.0.2.noarch                                      
  systemd-libs-252.16-1.amzn2023.0.1.aarch64                                    

Complete!
Finish(bootstrap): installing dnf tooling
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-aarch64-1704591447.273799/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.16.1.3-12.amzn2023.0.6.aarch64
  python3-dnf-4.12.0-2.amzn2023.0.4.noarch
  python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch
  yum-4.12.0-2.amzn2023.0.4.noarch
Start: installing minimal buildroot with dnf
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  43 kB/s | 1.5 kB     00:00    
Copr repository                                 2.4 MB/s | 172 kB     00:00    
Amazon Linux 2023 repository - aarch64           26 kB/s | 3.6 kB     00:00    
Dependencies resolved.
=============================================================================================
 Package                       Arch     Version                            Repository    Size
=============================================================================================
Installing:
 amazon-rpm-config             noarch   228-3.amzn2023.0.2                 amazonlinux   74 k
 bash                          aarch64  5.2.15-1.amzn2023.0.2              amazonlinux  1.8 M
 bzip2                         aarch64  1.0.8-6.amzn2023.0.2               amazonlinux   53 k
 coreutils                     aarch64  8.32-30.amzn2023.0.3               amazonlinux  1.2 M
 cpio                          aarch64  2.13-13.amzn2023.0.2               amazonlinux  270 k
 diffutils                     aarch64  3.8-1.amzn2023.0.2                 amazonlinux  368 k
 findutils                     aarch64  1:4.8.0-2.amzn2023.0.2             amazonlinux  541 k
 gawk                          aarch64  5.1.0-3.amzn2023.0.3               amazonlinux  984 k
 glibc-minimal-langpack        aarch64  2.34-52.amzn2023.0.7               amazonlinux   33 k
 grep                          aarch64  3.8-1.amzn2023.0.4                 amazonlinux  282 k
 gzip                          aarch64  1.12-1.amzn2023.0.1                amazonlinux  158 k
 info                          aarch64  6.7-10.amzn2023.0.2                amazonlinux  224 k
 patch                         aarch64  2.7.6-14.amzn2023.0.2              amazonlinux  126 k
 rpm-build                     aarch64  4.16.1.3-12.amzn2023.0.6           amazonlinux   92 k
 sed                           aarch64  4.8-7.amzn2023.0.2                 amazonlinux  295 k
 system-release                noarch   2023.3.20231218-0.amzn2023         amazonlinux   27 k
 tar                           aarch64  2:1.34-1.amzn2023.0.3              amazonlinux  869 k
 unzip                         aarch64  6.0-57.amzn2023.0.2                amazonlinux  180 k
 util-linux                    aarch64  2.37.4-1.amzn2023.0.3              amazonlinux  2.2 M
 which                         aarch64  2.21-26.amzn2023.0.2               amazonlinux   42 k
 xz                            aarch64  5.2.5-9.amzn2023.0.2               amazonlinux  216 k
Installing dependencies:
 alternatives                  aarch64  1.15-2.amzn2023.0.2                amazonlinux   36 k
 amazon-linux-repo-cdn         noarch   2023.3.20231218-0.amzn2023         amazonlinux   16 k
 audit-libs                    aarch64  3.0.6-1.amzn2023.0.2               amazonlinux  116 k
 basesystem                    noarch   11-11.amzn2023.0.2                 amazonlinux  7.8 k
 binutils                      aarch64  2.39-6.amzn2023.0.10               amazonlinux  4.7 M
 bzip2-libs                    aarch64  1.0.8-6.amzn2023.0.2               amazonlinux   44 k
 ca-certificates               noarch   2023.2.62-1.0.amzn2023.0.1         amazonlinux  739 k
 coreutils-common              aarch64  8.32-30.amzn2023.0.3               amazonlinux  2.0 M
 cracklib                      aarch64  2.9.6-27.amzn2023.0.2              amazonlinux   83 k
 crypto-policies               noarch   20220428-1.gitdfb10ea.amzn2023.0.2 amazonlinux   60 k
 curl                          aarch64  8.3.0-1.amzn2023.0.2               amazonlinux  351 k
 cyrus-sasl-lib                aarch64  2.1.27-18.amzn2023.0.3             amazonlinux  776 k
 dwz                           aarch64  0.14-6.amzn2023.0.2                amazonlinux  127 k
 ed                            aarch64  1.14.2-10.amzn2023.0.2             amazonlinux   74 k
 efi-srpm-macros               noarch   5-4.amzn2023.0.5                   amazonlinux   23 k
 elfutils                      aarch64  0.188-3.amzn2023.0.2               amazonlinux  519 k
 elfutils-debuginfod-client    aarch64  0.188-3.amzn2023.0.2               amazonlinux   41 k
 elfutils-default-yama-scope   noarch   0.188-3.amzn2023.0.2               amazonlinux   17 k
 elfutils-libelf               aarch64  0.188-3.amzn2023.0.2               amazonlinux  199 k
 elfutils-libs                 aarch64  0.188-3.amzn2023.0.2               amazonlinux  257 k
 file                          aarch64  5.39-7.amzn2023.0.4                amazonlinux   50 k
 file-libs                     aarch64  5.39-7.amzn2023.0.4                amazonlinux  587 k
 filesystem                    aarch64  3.14-5.amzn2023.0.3                amazonlinux   22 k
 fonts-srpm-macros             noarch   1:2.0.5-12.amzn2023.0.2            amazonlinux   27 k
 gdb-minimal                   aarch64  12.1-5.amzn2023.0.3                amazonlinux  3.5 M
 gdbm-libs                     aarch64  1:1.19-2.amzn2023.0.2              amazonlinux   53 k
 ghc-srpm-macros               noarch   1.5.0-4.amzn2023.0.2               amazonlinux  8.5 k
 glibc                         aarch64  2.34-52.amzn2023.0.7               amazonlinux  1.7 M
 glibc-common                  aarch64  2.34-52.amzn2023.0.7               amazonlinux  297 k
 glibc-gconv-extra             aarch64  2.34-52.amzn2023.0.7               amazonlinux  1.9 M
 gmp                           aarch64  1:6.2.1-2.amzn2023.0.2             amazonlinux  276 k
 go-srpm-macros                noarch   3.3.1-1.amzn2023                   copr_base     28 k
 jansson                       aarch64  2.14-0.amzn2023                    amazonlinux   47 k
 kernel-srpm-macros            noarch   1.0-14.amzn2023.0.2                amazonlinux   10 k
 keyutils-libs                 aarch64  1.6.3-1.amzn2023                   amazonlinux   33 k
 krb5-libs                     aarch64  1.21-3.amzn2023.0.3                amazonlinux  768 k
 libacl                        aarch64  2.3.1-2.amzn2023.0.2               amazonlinux   24 k
 libarchive                    aarch64  3.5.3-2.amzn2023.0.3               amazonlinux  395 k
 libattr                       aarch64  2.5.1-3.amzn2023.0.2               amazonlinux   19 k
 libblkid                      aarch64  2.37.4-1.amzn2023.0.3              amazonlinux  106 k
 libbrotli                     aarch64  1.0.9-4.amzn2023.0.2               amazonlinux  316 k
 libcap                        aarch64  2.48-2.amzn2023.0.3                amazonlinux   68 k
 libcap-ng                     aarch64  0.8.2-4.amzn2023.0.2               amazonlinux   33 k
 libcom_err                    aarch64  1.46.5-2.amzn2023.0.2              amazonlinux   27 k
 libcurl                       aarch64  8.3.0-1.amzn2023.0.2               amazonlinux  339 k
 libdb                         aarch64  5.3.28-49.amzn2023.0.2             amazonlinux  731 k
 libeconf                      aarch64  0.4.0-1.amzn2023.0.3               amazonlinux   27 k
 libfdisk                      aarch64  2.37.4-1.amzn2023.0.3              amazonlinux  149 k
 libffi                        aarch64  3.4.4-1.amzn2023.0.1               amazonlinux   37 k
 libgcc                        aarch64  11.4.1-2.amzn2023.0.2              amazonlinux   87 k
 libgomp                       aarch64  11.4.1-2.amzn2023.0.2              amazonlinux  262 k
 libidn2                       aarch64  2.3.2-1.amzn2023.0.5               amazonlinux  105 k
 libmount                      aarch64  2.37.4-1.amzn2023.0.3              amazonlinux  131 k
 libnghttp2                    aarch64  1.57.0-1.amzn2023.0.1              amazonlinux   77 k
 libpkgconf                    aarch64  1.8.0-4.amzn2023.0.2               amazonlinux   37 k
 libpsl                        aarch64  0.21.1-3.amzn2023.0.2              amazonlinux   61 k
 libpwquality                  aarch64  1.4.4-6.amzn2023.0.2               amazonlinux  106 k
 libselinux                    aarch64  3.4-5.amzn2023.0.2                 amazonlinux   87 k
 libsemanage                   aarch64  3.4-5.amzn2023.0.2                 amazonlinux  119 k
 libsepol                      aarch64  3.4-3.amzn2023.0.3                 amazonlinux  311 k
 libsigsegv                    aarch64  2.13-2.amzn2023.0.2                amazonlinux   28 k
 libsmartcols                  aarch64  2.37.4-1.amzn2023.0.3              amazonlinux   61 k
 libssh                        aarch64  0.10.5-1.amzn2023.0.2              amazonlinux  213 k
 libssh-config                 noarch   0.10.5-1.amzn2023.0.2              amazonlinux   11 k
 libstdc++                     aarch64  11.4.1-2.amzn2023.0.2              amazonlinux  691 k
 libtasn1                      aarch64  4.19.0-1.amzn2023.0.4              amazonlinux   75 k
 libunistring                  aarch64  0.9.10-10.amzn2023.0.2             amazonlinux  493 k
 libutempter                   aarch64  1.2.1-4.amzn2023.0.2               amazonlinux   27 k
 libuuid                       aarch64  2.37.4-1.amzn2023.0.3              amazonlinux   27 k
 libverto                      aarch64  0.3.2-1.amzn2023.0.2               amazonlinux   22 k
 libxcrypt                     aarch64  4.4.33-7.amzn2023                  amazonlinux  127 k
 libxml2                       aarch64  2.10.4-1.amzn2023.0.6              amazonlinux  691 k
 libzstd                       aarch64  1.5.5-1.amzn2023.0.1               amazonlinux  284 k
 lua-libs                      aarch64  5.4.4-3.amzn2023.0.2               amazonlinux  214 k
 lua-srpm-macros               noarch   1-4.amzn2023.0.2                   amazonlinux  9.2 k
 lz4-libs                      aarch64  1.9.4-1.amzn2023.0.2               amazonlinux   73 k
 mpfr                          aarch64  4.1.0-7.amzn2023.0.2               amazonlinux  243 k
 ncurses-base                  noarch   6.2-4.20200222.amzn2023.0.4        amazonlinux   60 k
 ncurses-libs                  aarch64  6.2-4.20200222.amzn2023.0.4        amazonlinux  318 k
 ocaml-srpm-macros             noarch   6-6.amzn2023.0.2                   amazonlinux  8.8 k
 openblas-srpm-macros          noarch   2-9.amzn2023.0.2                   amazonlinux  8.2 k
 openldap                      aarch64  2.4.57-6.amzn2023.0.6              amazonlinux  254 k
 openssl-libs                  aarch64  1:3.0.8-1.amzn2023.0.10            amazonlinux  2.1 M
 p11-kit                       aarch64  0.24.1-2.amzn2023.0.3              amazonlinux  346 k
 p11-kit-trust                 aarch64  0.24.1-2.amzn2023.0.3              amazonlinux  138 k
 package-notes-srpm-macros     noarch   0.4-18.amzn2023.0.5                amazonlinux   13 k
 pam                           aarch64  1.5.1-8.amzn2023.0.3               amazonlinux  554 k
 pcre2                         aarch64  10.40-1.amzn2023.0.3               amazonlinux  220 k
 pcre2-syntax                  noarch   10.40-1.amzn2023.0.3               amazonlinux  142 k
 perl-srpm-macros              noarch   1-39.amzn2023.0.2                  amazonlinux  8.7 k
 pkgconf                       aarch64  1.8.0-4.amzn2023.0.2               amazonlinux   43 k
 pkgconf-m4                    noarch   1.8.0-4.amzn2023.0.2               amazonlinux   15 k
 pkgconf-pkg-config            aarch64  1.8.0-4.amzn2023.0.2               amazonlinux   11 k
 popt                          aarch64  1.18-6.amzn2023.0.2                amazonlinux   59 k
 publicsuffix-list-dafsa       noarch   20221208-60.amzn2023               amazonlinux   61 k
 python-srpm-macros            noarch   3.9-41.amzn2023.0.5                amazonlinux   22 k
 readline                      aarch64  8.1-2.amzn2023.0.2                 amazonlinux  212 k
 rpm                           aarch64  4.16.1.3-12.amzn2023.0.6           amazonlinux  484 k
 rpm-build-libs                aarch64  4.16.1.3-12.amzn2023.0.6           amazonlinux   87 k
 rpm-libs                      aarch64  4.16.1.3-12.amzn2023.0.6           amazonlinux  305 k
 rust-srpm-macros              noarch   21-42.amzn2023.0.2                 amazonlinux   10 k
 setup                         noarch   2.13.7-3.amzn2023.0.2              amazonlinux  141 k
 shadow-utils                  aarch64  2:4.9-12.amzn2023.0.4              amazonlinux  1.1 M
 sqlite-libs                   aarch64  3.40.0-1.amzn2023.0.3              amazonlinux  660 k
 systemd-libs                  aarch64  252.16-1.amzn2023.0.1              amazonlinux  597 k
 util-linux-core               aarch64  2.37.4-1.amzn2023.0.3              amazonlinux  438 k
 xxhash-libs                   aarch64  0.8.0-3.amzn2023.0.2               amazonlinux   32 k
 xz-libs                       aarch64  5.2.5-9.amzn2023.0.2               amazonlinux   92 k
 zip                           aarch64  3.0-28.amzn2023.0.2                amazonlinux  254 k
 zlib                          aarch64  1.2.11-33.amzn2023.0.5             amazonlinux   91 k
 zstd                          aarch64  1.5.5-1.amzn2023.0.1               amazonlinux  450 k

Transaction Summary
=============================================================================================
Install  132 Packages

Total size: 45 M
Installed size: 284 M
Downloading Packages:
[SKIPPED] go-srpm-macros-3.3.1-1.amzn2023.noarch.rpm: Already downloaded       
[SKIPPED] efi-srpm-macros-5-4.amzn2023.0.5.noarch.rpm: Already downloaded      
[SKIPPED] ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch.rpm: Already downloaded  
[SKIPPED] elfutils-default-yama-scope-0.188-3.amzn2023.0.2.noarch.rpm: Already downloaded
[SKIPPED] ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch.rpm: Already downloaded
[SKIPPED] openblas-srpm-macros-2-9.amzn2023.0.2.noarch.rpm: Already downloaded 
[SKIPPED] publicsuffix-list-dafsa-20221208-60.amzn2023.noarch.rpm: Already downloaded
[SKIPPED] kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch.rpm: Already downloaded
[SKIPPED] pcre2-syntax-10.40-1.amzn2023.0.3.noarch.rpm: Already downloaded     
[SKIPPED] ocaml-srpm-macros-6-6.amzn2023.0.2.noarch.rpm: Already downloaded    
[SKIPPED] basesystem-11-11.amzn2023.0.2.noarch.rpm: Already downloaded         
[SKIPPED] setup-2.13.7-3.amzn2023.0.2.noarch.rpm: Already downloaded           
[SKIPPED] libssh-config-0.10.5-1.amzn2023.0.2.noarch.rpm: Already downloaded   
[SKIPPED] amazon-rpm-config-228-3.amzn2023.0.2.noarch.rpm: Already downloaded  
[SKIPPED] ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarch.rpm: Already downloaded
[SKIPPED] python-srpm-macros-3.9-41.amzn2023.0.5.noarch.rpm: Already downloaded
[SKIPPED] crypto-policies-20220428-1.gitdfb10ea.amzn2023.0.2.noarch.rpm: Already downloaded
[SKIPPED] fonts-srpm-macros-2.0.5-12.amzn2023.0.2.noarch.rpm: Already downloaded
[SKIPPED] package-notes-srpm-macros-0.4-18.amzn2023.0.5.noarch.rpm: Already downloaded
[SKIPPED] perl-srpm-macros-1-39.amzn2023.0.2.noarch.rpm: Already downloaded    
[SKIPPED] lua-srpm-macros-1-4.amzn2023.0.2.noarch.rpm: Already downloaded      
[SKIPPED] system-release-2023.3.20231218-0.amzn2023.noarch.rpm: Already downloaded
[SKIPPED] amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023.noarch.rpm: Already downloaded
[SKIPPED] rust-srpm-macros-21-42.amzn2023.0.2.noarch.rpm: Already downloaded   
[SKIPPED] pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch.rpm: Already downloaded       
[SKIPPED] libzstd-1.5.5-1.amzn2023.0.1.aarch64.rpm: Already downloaded         
[SKIPPED] mpfr-4.1.0-7.amzn2023.0.2.aarch64.rpm: Already downloaded            
[SKIPPED] libverto-0.3.2-1.amzn2023.0.2.aarch64.rpm: Already downloaded        
[SKIPPED] elfutils-libelf-0.188-3.amzn2023.0.2.aarch64.rpm: Already downloaded 
[SKIPPED] ncurses-libs-6.2-4.20200222.amzn2023.0.4.aarch64.rpm: Already downloaded
[SKIPPED] bash-5.2.15-1.amzn2023.0.2.aarch64.rpm: Already downloaded           
[SKIPPED] diffutils-3.8-1.amzn2023.0.2.aarch64.rpm: Already downloaded         
[SKIPPED] p11-kit-trust-0.24.1-2.amzn2023.0.3.aarch64.rpm: Already downloaded  
[SKIPPED] util-linux-core-2.37.4-1.amzn2023.0.3.aarch64.rpm: Already downloaded
[SKIPPED] dwz-0.14-6.amzn2023.0.2.aarch64.rpm: Already downloaded              
[SKIPPED] libbrotli-1.0.9-4.amzn2023.0.2.aarch64.rpm: Already downloaded       
[SKIPPED] gawk-5.1.0-3.amzn2023.0.3.aarch64.rpm: Already downloaded            
[SKIPPED] findutils-4.8.0-2.amzn2023.0.2.aarch64.rpm: Already downloaded       
[SKIPPED] libffi-3.4.4-1.amzn2023.0.1.aarch64.rpm: Already downloaded          
[SKIPPED] rpm-build-4.16.1.3-12.amzn2023.0.6.aarch64.rpm: Already downloaded   
[SKIPPED] bzip2-libs-1.0.8-6.amzn2023.0.2.aarch64.rpm: Already downloaded      
[SKIPPED] pcre2-10.40-1.amzn2023.0.3.aarch64.rpm: Already downloaded           
[SKIPPED] popt-1.18-6.amzn2023.0.2.aarch64.rpm: Already downloaded             
[SKIPPED] elfutils-debuginfod-client-0.188-3.amzn2023.0.2.aarch64.rpm: Already downloaded
[SKIPPED] keyutils-libs-1.6.3-1.amzn2023.aarch64.rpm: Already downloaded       
[SKIPPED] gmp-6.2.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded             
[SKIPPED] glibc-common-2.34-52.amzn2023.0.7.aarch64.rpm: Already downloaded    
[SKIPPED] libsigsegv-2.13-2.amzn2023.0.2.aarch64.rpm: Already downloaded       
[SKIPPED] readline-8.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded          
[SKIPPED] elfutils-0.188-3.amzn2023.0.2.aarch64.rpm: Already downloaded        
[SKIPPED] libeconf-0.4.0-1.amzn2023.0.3.aarch64.rpm: Already downloaded        
[SKIPPED] libutempter-1.2.1-4.amzn2023.0.2.aarch64.rpm: Already downloaded     
[SKIPPED] filesystem-3.14-5.amzn2023.0.3.aarch64.rpm: Already downloaded       
[SKIPPED] coreutils-common-8.32-30.amzn2023.0.3.aarch64.rpm: Already downloaded
[SKIPPED] elfutils-libs-0.188-3.amzn2023.0.2.aarch64.rpm: Already downloaded   
[SKIPPED] libblkid-2.37.4-1.amzn2023.0.3.aarch64.rpm: Already downloaded       
[SKIPPED] libselinux-3.4-5.amzn2023.0.2.aarch64.rpm: Already downloaded        
[SKIPPED] audit-libs-3.0.6-1.amzn2023.0.2.aarch64.rpm: Already downloaded      
[SKIPPED] zlib-1.2.11-33.amzn2023.0.5.aarch64.rpm: Already downloaded          
[SKIPPED] rpm-build-libs-4.16.1.3-12.amzn2023.0.6.aarch64.rpm: Already downloaded
[SKIPPED] unzip-6.0-57.amzn2023.0.2.aarch64.rpm: Already downloaded            
[SKIPPED] libsmartcols-2.37.4-1.amzn2023.0.3.aarch64.rpm: Already downloaded   
[SKIPPED] patch-2.7.6-14.amzn2023.0.2.aarch64.rpm: Already downloaded          
[SKIPPED] cpio-2.13-13.amzn2023.0.2.aarch64.rpm: Already downloaded            
[SKIPPED] coreutils-8.32-30.amzn2023.0.3.aarch64.rpm: Already downloaded       
[SKIPPED] tar-1.34-1.amzn2023.0.3.aarch64.rpm: Already downloaded              
[SKIPPED] lua-libs-5.4.4-3.amzn2023.0.2.aarch64.rpm: Already downloaded        
[SKIPPED] libcap-2.48-2.amzn2023.0.3.aarch64.rpm: Already downloaded           
[SKIPPED] util-linux-2.37.4-1.amzn2023.0.3.aarch64.rpm: Already downloaded     
[SKIPPED] libpkgconf-1.8.0-4.amzn2023.0.2.aarch64.rpm: Already downloaded      
[SKIPPED] libacl-2.3.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded          
[SKIPPED] systemd-libs-252.16-1.amzn2023.0.1.aarch64.rpm: Already downloaded   
[SKIPPED] libfdisk-2.37.4-1.amzn2023.0.3.aarch64.rpm: Already downloaded       
[SKIPPED] libstdc++-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded      
[SKIPPED] which-2.21-26.amzn2023.0.2.aarch64.rpm: Already downloaded           
[SKIPPED] libtasn1-4.19.0-1.amzn2023.0.4.aarch64.rpm: Already downloaded       
[SKIPPED] file-libs-5.39-7.amzn2023.0.4.aarch64.rpm: Already downloaded        
[SKIPPED] zip-3.0-28.amzn2023.0.2.aarch64.rpm: Already downloaded              
[SKIPPED] lz4-libs-1.9.4-1.amzn2023.0.2.aarch64.rpm: Already downloaded        
[SKIPPED] p11-kit-0.24.1-2.amzn2023.0.3.aarch64.rpm: Already downloaded        
[SKIPPED] libssh-0.10.5-1.amzn2023.0.2.aarch64.rpm: Already downloaded         
[SKIPPED] sqlite-libs-3.40.0-1.amzn2023.0.3.aarch64.rpm: Already downloaded    
[SKIPPED] libcap-ng-0.8.2-4.amzn2023.0.2.aarch64.rpm: Already downloaded       
[SKIPPED] libattr-2.5.1-3.amzn2023.0.2.aarch64.rpm: Already downloaded         
[SKIPPED] sed-4.8-7.amzn2023.0.2.aarch64.rpm: Already downloaded               
[SKIPPED] openldap-2.4.57-6.amzn2023.0.6.aarch64.rpm: Already downloaded       
[SKIPPED] gdb-minimal-12.1-5.amzn2023.0.3.aarch64.rpm: Already downloaded      
[SKIPPED] zstd-1.5.5-1.amzn2023.0.1.aarch64.rpm: Already downloaded            
[SKIPPED] rpm-4.16.1.3-12.amzn2023.0.6.aarch64.rpm: Already downloaded         
[SKIPPED] libsemanage-3.4-5.amzn2023.0.2.aarch64.rpm: Already downloaded       
[SKIPPED] glibc-2.34-52.amzn2023.0.7.aarch64.rpm: Already downloaded           
[SKIPPED] libunistring-0.9.10-10.amzn2023.0.2.aarch64.rpm: Already downloaded  
[SKIPPED] xxhash-libs-0.8.0-3.amzn2023.0.2.aarch64.rpm: Already downloaded     
[SKIPPED] libdb-5.3.28-49.amzn2023.0.2.aarch64.rpm: Already downloaded         
[SKIPPED] pkgconf-1.8.0-4.amzn2023.0.2.aarch64.rpm: Already downloaded         
[SKIPPED] libcurl-8.3.0-1.amzn2023.0.2.aarch64.rpm: Already downloaded         
[SKIPPED] libidn2-2.3.2-1.amzn2023.0.5.aarch64.rpm: Already downloaded         
[SKIPPED] libcom_err-1.46.5-2.amzn2023.0.2.aarch64.rpm: Already downloaded     
[SKIPPED] bzip2-1.0.8-6.amzn2023.0.2.aarch64.rpm: Already downloaded           
[SKIPPED] libarchive-3.5.3-2.amzn2023.0.3.aarch64.rpm: Already downloaded      
[SKIPPED] gzip-1.12-1.amzn2023.0.1.aarch64.rpm: Already downloaded             
[SKIPPED] curl-8.3.0-1.amzn2023.0.2.aarch64.rpm: Already downloaded            
[SKIPPED] krb5-libs-1.21-3.amzn2023.0.3.aarch64.rpm: Already downloaded        
[SKIPPED] libnghttp2-1.57.0-1.amzn2023.0.1.aarch64.rpm: Already downloaded     
[SKIPPED] libmount-2.37.4-1.amzn2023.0.3.aarch64.rpm: Already downloaded       
[SKIPPED] xz-libs-5.2.5-9.amzn2023.0.2.aarch64.rpm: Already downloaded         
[SKIPPED] glibc-gconv-extra-2.34-52.amzn2023.0.7.aarch64.rpm: Already downloaded
[SKIPPED] jansson-2.14-0.amzn2023.aarch64.rpm: Already downloaded              
[SKIPPED] libgomp-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded        
[SKIPPED] libuuid-2.37.4-1.amzn2023.0.3.aarch64.rpm: Already downloaded        
[SKIPPED] glibc-minimal-langpack-2.34-52.amzn2023.0.7.aarch64.rpm: Already downloaded
[SKIPPED] libsepol-3.4-3.amzn2023.0.3.aarch64.rpm: Already downloaded          
[SKIPPED] cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.aarch64.rpm: Already downloaded
[SKIPPED] pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.aarch64.rpm: Already downloaded
[SKIPPED] libpwquality-1.4.4-6.amzn2023.0.2.aarch64.rpm: Already downloaded    
[SKIPPED] ed-1.14.2-10.amzn2023.0.2.aarch64.rpm: Already downloaded            
[SKIPPED] shadow-utils-4.9-12.amzn2023.0.4.aarch64.rpm: Already downloaded     
[SKIPPED] libgcc-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded         
[SKIPPED] gdbm-libs-1.19-2.amzn2023.0.2.aarch64.rpm: Already downloaded        
[SKIPPED] libxcrypt-4.4.33-7.amzn2023.aarch64.rpm: Already downloaded          
[SKIPPED] binutils-2.39-6.amzn2023.0.10.aarch64.rpm: Already downloaded        
[SKIPPED] pam-1.5.1-8.amzn2023.0.3.aarch64.rpm: Already downloaded             
[SKIPPED] rpm-libs-4.16.1.3-12.amzn2023.0.6.aarch64.rpm: Already downloaded    
[SKIPPED] grep-3.8-1.amzn2023.0.4.aarch64.rpm: Already downloaded              
[SKIPPED] libpsl-0.21.1-3.amzn2023.0.2.aarch64.rpm: Already downloaded         
[SKIPPED] libxml2-2.10.4-1.amzn2023.0.6.aarch64.rpm: Already downloaded        
[SKIPPED] alternatives-1.15-2.amzn2023.0.2.aarch64.rpm: Already downloaded     
[SKIPPED] info-6.7-10.amzn2023.0.2.aarch64.rpm: Already downloaded             
[SKIPPED] file-5.39-7.amzn2023.0.4.aarch64.rpm: Already downloaded             
[SKIPPED] openssl-libs-3.0.8-1.amzn2023.0.10.aarch64.rpm: Already downloaded   
[SKIPPED] xz-5.2.5-9.amzn2023.0.2.aarch64.rpm: Already downloaded              
[SKIPPED] cracklib-2.9.6-27.amzn2023.0.2.aarch64.rpm: Already downloaded       
Amazon Linux 2023 repository - aarch64          1.7 MB/s | 1.8 kB     00:00    
Importing GPG key 0xD832C631:
 Userid     : "Amazon Linux <amazon-linux@amazon.com>"
 Fingerprint: B21C 50FA 44A9 9720 EAA7 2F7F E951 904A D832 C631
 From       : /usr/share/distribution-gpg-keys/amazon-linux/RPM-GPG-KEY-amazon-linux-2023
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.14-5.amzn2023.0.3.aarch64                 1/1 
  Preparing        :                                                        1/1 
  Installing       : libgcc-11.4.1-2.amzn2023.0.2.aarch64                 1/132 
  Running scriptlet: libgcc-11.4.1-2.amzn2023.0.2.aarch64                 1/132 
  Installing       : crypto-policies-20220428-1.gitdfb10ea.amzn2023.0     2/132 
  Running scriptlet: crypto-policies-20220428-1.gitdfb10ea.amzn2023.0     2/132 
  Installing       : coreutils-common-8.32-30.amzn2023.0.3.aarch64        3/132 
  Installing       : pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch               4/132 
  Installing       : rust-srpm-macros-21-42.amzn2023.0.2.noarch           5/132 
  Installing       : perl-srpm-macros-1-39.amzn2023.0.2.noarch            6/132 
  Installing       : libssh-config-0.10.5-1.amzn2023.0.2.noarch           7/132 
  Installing       : ocaml-srpm-macros-6-6.amzn2023.0.2.noarch            8/132 
  Installing       : pcre2-syntax-10.40-1.amzn2023.0.3.noarch             9/132 
  Installing       : kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch       10/132 
  Installing       : publicsuffix-list-dafsa-20221208-60.amzn2023.noa    11/132 
  Installing       : openblas-srpm-macros-2-9.amzn2023.0.2.noarch        12/132 
  Installing       : ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch     13/132 
  Installing       : amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023    14/132 
  Installing       : ncurses-libs-6.2-4.20200222.amzn2023.0.4.aarch64    15/132 
  Installing       : system-release-2023.3.20231218-0.amzn2023.noarch    16/132 
  Installing       : setup-2.13.7-3.amzn2023.0.2.noarch                  17/132 
warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.13.7-3.amzn2023.0.2.noarch                  17/132 
  Installing       : filesystem-3.14-5.amzn2023.0.3.aarch64              18/132 
  Installing       : basesystem-11-11.amzn2023.0.2.noarch                19/132 
  Installing       : bash-5.2.15-1.amzn2023.0.2.aarch64                  20/132 
  Running scriptlet: bash-5.2.15-1.amzn2023.0.2.aarch64                  20/132 
  Installing       : glibc-gconv-extra-2.34-52.amzn2023.0.7.aarch64      21/132 
  Running scriptlet: glibc-gconv-extra-2.34-52.amzn2023.0.7.aarch64      21/132 
  Installing       : glibc-minimal-langpack-2.34-52.amzn2023.0.7.aarc    22/132 
  Installing       : glibc-common-2.34-52.amzn2023.0.7.aarch64           23/132 
  Running scriptlet: glibc-2.34-52.amzn2023.0.7.aarch64                  24/132 
  Installing       : glibc-2.34-52.amzn2023.0.7.aarch64                  24/132 
  Running scriptlet: glibc-2.34-52.amzn2023.0.7.aarch64                  24/132 
  Installing       : zlib-1.2.11-33.amzn2023.0.5.aarch64                 25/132 
  Installing       : xz-libs-5.2.5-9.amzn2023.0.2.aarch64                26/132 
  Installing       : bzip2-libs-1.0.8-6.amzn2023.0.2.aarch64             27/132 
  Installing       : elfutils-libelf-0.188-3.amzn2023.0.2.aarch64        28/132 
  Installing       : libuuid-2.37.4-1.amzn2023.0.3.aarch64               29/132 
  Installing       : libzstd-1.5.5-1.amzn2023.0.1.aarch64                30/132 
  Installing       : popt-1.18-6.amzn2023.0.2.aarch64                    31/132 
  Installing       : gmp-1:6.2.1-2.amzn2023.0.2.aarch64                  32/132 
  Installing       : libcap-2.48-2.amzn2023.0.3.aarch64                  33/132 
  Installing       : libattr-2.5.1-3.amzn2023.0.2.aarch64                34/132 
  Installing       : libacl-2.3.1-2.amzn2023.0.2.aarch64                 35/132 
  Installing       : libxcrypt-4.4.33-7.amzn2023.aarch64                 36/132 
  Installing       : readline-8.1-2.amzn2023.0.2.aarch64                 37/132 
  Installing       : libstdc++-11.4.1-2.amzn2023.0.2.aarch64             38/132 
  Installing       : systemd-libs-252.16-1.amzn2023.0.1.aarch64          39/132 
  Installing       : mpfr-4.1.0-7.amzn2023.0.2.aarch64                   40/132 
  Installing       : unzip-6.0-57.amzn2023.0.2.aarch64                   41/132 
  Installing       : file-libs-5.39-7.amzn2023.0.4.aarch64               42/132 
  Installing       : file-5.39-7.amzn2023.0.4.aarch64                    43/132 
  Installing       : sqlite-libs-3.40.0-1.amzn2023.0.3.aarch64           44/132 
  Installing       : pcre2-10.40-1.amzn2023.0.3.aarch64                  45/132 
  Installing       : grep-3.8-1.amzn2023.0.4.aarch64                     46/132 
  Installing       : libsmartcols-2.37.4-1.amzn2023.0.3.aarch64          47/132 
  Installing       : lua-libs-5.4.4-3.amzn2023.0.2.aarch64               48/132 
  Installing       : lz4-libs-1.9.4-1.amzn2023.0.2.aarch64               49/132 
  Installing       : libcap-ng-0.8.2-4.amzn2023.0.2.aarch64              50/132 
  Installing       : audit-libs-3.0.6-1.amzn2023.0.2.aarch64             51/132 
  Installing       : libunistring-0.9.10-10.amzn2023.0.2.aarch64         52/132 
  Installing       : libidn2-2.3.2-1.amzn2023.0.5.aarch64                53/132 
  Installing       : libcom_err-1.46.5-2.amzn2023.0.2.aarch64            54/132 
  Installing       : libsepol-3.4-3.amzn2023.0.3.aarch64                 55/132 
  Installing       : libselinux-3.4-5.amzn2023.0.2.aarch64               56/132 
  Installing       : sed-4.8-7.amzn2023.0.2.aarch64                      57/132 
  Installing       : findutils-1:4.8.0-2.amzn2023.0.2.aarch64            58/132 
  Installing       : alternatives-1.15-2.amzn2023.0.2.aarch64            59/132 
  Installing       : tar-2:1.34-1.amzn2023.0.3.aarch64                   60/132 
  Installing       : libsemanage-3.4-5.amzn2023.0.2.aarch64              61/132 
  Installing       : shadow-utils-2:4.9-12.amzn2023.0.4.aarch64          62/132 
  Running scriptlet: libutempter-1.2.1-4.amzn2023.0.2.aarch64            63/132 
  Installing       : libutempter-1.2.1-4.amzn2023.0.2.aarch64            63/132 
  Installing       : libpsl-0.21.1-3.amzn2023.0.2.aarch64                64/132 
  Installing       : zstd-1.5.5-1.amzn2023.0.1.aarch64                   65/132 
  Installing       : xz-5.2.5-9.amzn2023.0.2.aarch64                     66/132 
  Installing       : zip-3.0-28.amzn2023.0.2.aarch64                     67/132 
  Installing       : dwz-0.14-6.amzn2023.0.2.aarch64                     68/132 
  Installing       : bzip2-1.0.8-6.amzn2023.0.2.aarch64                  69/132 
  Installing       : libxml2-2.10.4-1.amzn2023.0.6.aarch64               70/132 
  Installing       : info-6.7-10.amzn2023.0.2.aarch64                    71/132 
  Installing       : ed-1.14.2-10.amzn2023.0.2.aarch64                   72/132 
  Installing       : patch-2.7.6-14.amzn2023.0.2.aarch64                 73/132 
  Installing       : libverto-0.3.2-1.amzn2023.0.2.aarch64               74/132 
  Installing       : diffutils-3.8-1.amzn2023.0.2.aarch64                75/132 
  Installing       : libbrotli-1.0.9-4.amzn2023.0.2.aarch64              76/132 
  Installing       : libffi-3.4.4-1.amzn2023.0.1.aarch64                 77/132 
  Installing       : p11-kit-0.24.1-2.amzn2023.0.3.aarch64               78/132 
  Installing       : keyutils-libs-1.6.3-1.amzn2023.aarch64              79/132 
  Installing       : libsigsegv-2.13-2.amzn2023.0.2.aarch64              80/132 
  Installing       : gawk-5.1.0-3.amzn2023.0.3.aarch64                   81/132 
  Installing       : libeconf-0.4.0-1.amzn2023.0.3.aarch64               82/132 
  Installing       : cpio-2.13-13.amzn2023.0.2.aarch64                   83/132 
  Installing       : libpkgconf-1.8.0-4.amzn2023.0.2.aarch64             84/132 
  Installing       : libtasn1-4.19.0-1.amzn2023.0.4.aarch64              85/132 
  Installing       : p11-kit-trust-0.24.1-2.amzn2023.0.3.aarch64         86/132 
  Running scriptlet: p11-kit-trust-0.24.1-2.amzn2023.0.3.aarch64         86/132 
  Installing       : openssl-libs-1:3.0.8-1.amzn2023.0.10.aarch64        87/132 
  Installing       : coreutils-8.32-30.amzn2023.0.3.aarch64              88/132 
  Running scriptlet: ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc    89/132 
  Installing       : ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc    89/132 
  Running scriptlet: ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc    89/132 
  Installing       : libblkid-2.37.4-1.amzn2023.0.3.aarch64              90/132 
  Running scriptlet: libblkid-2.37.4-1.amzn2023.0.3.aarch64              90/132 
  Installing       : krb5-libs-1.21-3.amzn2023.0.3.aarch64               91/132 
  Installing       : libmount-2.37.4-1.amzn2023.0.3.aarch64              92/132 
  Installing       : gzip-1.12-1.amzn2023.0.1.aarch64                    93/132 
  Installing       : cracklib-2.9.6-27.amzn2023.0.2.aarch64              94/132 
  Installing       : util-linux-core-2.37.4-1.amzn2023.0.3.aarch64       95/132 
  Running scriptlet: util-linux-core-2.37.4-1.amzn2023.0.3.aarch64       95/132 
  Installing       : libssh-0.10.5-1.amzn2023.0.2.aarch64                96/132 
  Installing       : libfdisk-2.37.4-1.amzn2023.0.3.aarch64              97/132 
  Installing       : libarchive-3.5.3-2.amzn2023.0.3.aarch64             98/132 
  Installing       : xxhash-libs-0.8.0-3.amzn2023.0.2.aarch64            99/132 
  Installing       : libdb-5.3.28-49.amzn2023.0.2.aarch64               100/132 
  Installing       : pam-1.5.1-8.amzn2023.0.3.aarch64                   101/132 
  Installing       : libpwquality-1.4.4-6.amzn2023.0.2.aarch64          102/132 
  Installing       : libnghttp2-1.57.0-1.amzn2023.0.1.aarch64           103/132 
  Installing       : jansson-2.14-0.amzn2023.aarch64                    104/132 
  Installing       : libgomp-11.4.1-2.amzn2023.0.2.aarch64              105/132 
  Installing       : gdbm-libs-1:1.19-2.amzn2023.0.2.aarch64            106/132 
  Installing       : cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.aarch64      107/132 
  Installing       : openldap-2.4.57-6.amzn2023.0.6.aarch64             108/132 
  Installing       : libcurl-8.3.0-1.amzn2023.0.2.aarch64               109/132 
  Installing       : curl-8.3.0-1.amzn2023.0.2.aarch64                  110/132 
  Installing       : rpm-libs-4.16.1.3-12.amzn2023.0.6.aarch64          111/132 
  Installing       : rpm-4.16.1.3-12.amzn2023.0.6.aarch64               112/132 
  Installing       : efi-srpm-macros-5-4.amzn2023.0.5.noarch            113/132 
  Installing       : lua-srpm-macros-1-4.amzn2023.0.2.noarch            114/132 
  Installing       : elfutils-default-yama-scope-0.188-3.amzn2023.0.2   115/132 
  Running scriptlet: elfutils-default-yama-scope-0.188-3.amzn2023.0.2   115/132 
  Installing       : elfutils-debuginfod-client-0.188-3.amzn2023.0.2.   116/132 
  Installing       : elfutils-libs-0.188-3.amzn2023.0.2.aarch64         117/132 
  Installing       : elfutils-0.188-3.amzn2023.0.2.aarch64              118/132 
  Installing       : rpm-build-libs-4.16.1.3-12.amzn2023.0.6.aarch64    119/132 
  Installing       : gdb-minimal-12.1-5.amzn2023.0.3.aarch64            120/132 
  Installing       : binutils-2.39-6.amzn2023.0.10.aarch64              121/132 
  Running scriptlet: binutils-2.39-6.amzn2023.0.10.aarch64              121/132 
  Installing       : package-notes-srpm-macros-0.4-18.amzn2023.0.5.no   122/132 
  Installing       : ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch        123/132 
  Installing       : python-srpm-macros-3.9-41.amzn2023.0.5.noarch      124/132 
  Installing       : fonts-srpm-macros-1:2.0.5-12.amzn2023.0.2.noarch   125/132 
  Installing       : amazon-rpm-config-228-3.amzn2023.0.2.noarch        126/132 
  Running scriptlet: amazon-rpm-config-228-3.amzn2023.0.2.noarch        126/132 
  Installing       : go-srpm-macros-3.3.1-1.amzn2023.noarch             127/132 
  Installing       : pkgconf-1.8.0-4.amzn2023.0.2.aarch64               128/132 
  Installing       : pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.aarch64    129/132 
  Installing       : rpm-build-4.16.1.3-12.amzn2023.0.6.aarch64         130/132 
  Installing       : util-linux-2.37.4-1.amzn2023.0.3.aarch64           131/132 
  Running scriptlet: util-linux-2.37.4-1.amzn2023.0.3.aarch64           131/132 
  Installing       : which-2.21-26.amzn2023.0.2.aarch64                 132/132 
  Running scriptlet: filesystem-3.14-5.amzn2023.0.3.aarch64             132/132 
  Running scriptlet: ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc   132/132 
  Running scriptlet: pam-1.5.1-8.amzn2023.0.3.aarch64                   132/132 
  Running scriptlet: rpm-4.16.1.3-12.amzn2023.0.6.aarch64               132/132 
  Running scriptlet: which-2.21-26.amzn2023.0.2.aarch64                 132/132 
  Verifying        : go-srpm-macros-3.3.1-1.amzn2023.noarch               1/132 
  Verifying        : efi-srpm-macros-5-4.amzn2023.0.5.noarch              2/132 
  Verifying        : ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch          3/132 
  Verifying        : elfutils-default-yama-scope-0.188-3.amzn2023.0.2     4/132 
  Verifying        : ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch      5/132 
  Verifying        : openblas-srpm-macros-2-9.amzn2023.0.2.noarch         6/132 
  Verifying        : publicsuffix-list-dafsa-20221208-60.amzn2023.noa     7/132 
  Verifying        : kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch        8/132 
  Verifying        : pcre2-syntax-10.40-1.amzn2023.0.3.noarch             9/132 
  Verifying        : ocaml-srpm-macros-6-6.amzn2023.0.2.noarch           10/132 
  Verifying        : basesystem-11-11.amzn2023.0.2.noarch                11/132 
  Verifying        : setup-2.13.7-3.amzn2023.0.2.noarch                  12/132 
  Verifying        : libssh-config-0.10.5-1.amzn2023.0.2.noarch          13/132 
  Verifying        : amazon-rpm-config-228-3.amzn2023.0.2.noarch         14/132 
  Verifying        : ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc    15/132 
  Verifying        : python-srpm-macros-3.9-41.amzn2023.0.5.noarch       16/132 
  Verifying        : crypto-policies-20220428-1.gitdfb10ea.amzn2023.0    17/132 
  Verifying        : fonts-srpm-macros-1:2.0.5-12.amzn2023.0.2.noarch    18/132 
  Verifying        : package-notes-srpm-macros-0.4-18.amzn2023.0.5.no    19/132 
  Verifying        : perl-srpm-macros-1-39.amzn2023.0.2.noarch           20/132 
  Verifying        : lua-srpm-macros-1-4.amzn2023.0.2.noarch             21/132 
  Verifying        : system-release-2023.3.20231218-0.amzn2023.noarch    22/132 
  Verifying        : amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023    23/132 
  Verifying        : rust-srpm-macros-21-42.amzn2023.0.2.noarch          24/132 
  Verifying        : pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch              25/132 
  Verifying        : libzstd-1.5.5-1.amzn2023.0.1.aarch64                26/132 
  Verifying        : mpfr-4.1.0-7.amzn2023.0.2.aarch64                   27/132 
  Verifying        : libverto-0.3.2-1.amzn2023.0.2.aarch64               28/132 
  Verifying        : elfutils-libelf-0.188-3.amzn2023.0.2.aarch64        29/132 
  Verifying        : ncurses-libs-6.2-4.20200222.amzn2023.0.4.aarch64    30/132 
  Verifying        : bash-5.2.15-1.amzn2023.0.2.aarch64                  31/132 
  Verifying        : diffutils-3.8-1.amzn2023.0.2.aarch64                32/132 
  Verifying        : p11-kit-trust-0.24.1-2.amzn2023.0.3.aarch64         33/132 
  Verifying        : util-linux-core-2.37.4-1.amzn2023.0.3.aarch64       34/132 
  Verifying        : dwz-0.14-6.amzn2023.0.2.aarch64                     35/132 
  Verifying        : libbrotli-1.0.9-4.amzn2023.0.2.aarch64              36/132 
  Verifying        : gawk-5.1.0-3.amzn2023.0.3.aarch64                   37/132 
  Verifying        : findutils-1:4.8.0-2.amzn2023.0.2.aarch64            38/132 
  Verifying        : libffi-3.4.4-1.amzn2023.0.1.aarch64                 39/132 
  Verifying        : rpm-build-4.16.1.3-12.amzn2023.0.6.aarch64          40/132 
  Verifying        : bzip2-libs-1.0.8-6.amzn2023.0.2.aarch64             41/132 
  Verifying        : pcre2-10.40-1.amzn2023.0.3.aarch64                  42/132 
  Verifying        : popt-1.18-6.amzn2023.0.2.aarch64                    43/132 
  Verifying        : elfutils-debuginfod-client-0.188-3.amzn2023.0.2.    44/132 
  Verifying        : keyutils-libs-1.6.3-1.amzn2023.aarch64              45/132 
  Verifying        : gmp-1:6.2.1-2.amzn2023.0.2.aarch64                  46/132 
  Verifying        : glibc-common-2.34-52.amzn2023.0.7.aarch64           47/132 
  Verifying        : libsigsegv-2.13-2.amzn2023.0.2.aarch64              48/132 
  Verifying        : readline-8.1-2.amzn2023.0.2.aarch64                 49/132 
  Verifying        : elfutils-0.188-3.amzn2023.0.2.aarch64               50/132 
  Verifying        : libeconf-0.4.0-1.amzn2023.0.3.aarch64               51/132 
  Verifying        : libutempter-1.2.1-4.amzn2023.0.2.aarch64            52/132 
  Verifying        : filesystem-3.14-5.amzn2023.0.3.aarch64              53/132 
  Verifying        : coreutils-common-8.32-30.amzn2023.0.3.aarch64       54/132 
  Verifying        : elfutils-libs-0.188-3.amzn2023.0.2.aarch64          55/132 
  Verifying        : libblkid-2.37.4-1.amzn2023.0.3.aarch64              56/132 
  Verifying        : libselinux-3.4-5.amzn2023.0.2.aarch64               57/132 
  Verifying        : audit-libs-3.0.6-1.amzn2023.0.2.aarch64             58/132 
  Verifying        : zlib-1.2.11-33.amzn2023.0.5.aarch64                 59/132 
  Verifying        : rpm-build-libs-4.16.1.3-12.amzn2023.0.6.aarch64     60/132 
  Verifying        : unzip-6.0-57.amzn2023.0.2.aarch64                   61/132 
  Verifying        : libsmartcols-2.37.4-1.amzn2023.0.3.aarch64          62/132 
  Verifying        : patch-2.7.6-14.amzn2023.0.2.aarch64                 63/132 
  Verifying        : cpio-2.13-13.amzn2023.0.2.aarch64                   64/132 
  Verifying        : coreutils-8.32-30.amzn2023.0.3.aarch64              65/132 
  Verifying        : tar-2:1.34-1.amzn2023.0.3.aarch64                   66/132 
  Verifying        : lua-libs-5.4.4-3.amzn2023.0.2.aarch64               67/132 
  Verifying        : libcap-2.48-2.amzn2023.0.3.aarch64                  68/132 
  Verifying        : util-linux-2.37.4-1.amzn2023.0.3.aarch64            69/132 
  Verifying        : libpkgconf-1.8.0-4.amzn2023.0.2.aarch64             70/132 
  Verifying        : libacl-2.3.1-2.amzn2023.0.2.aarch64                 71/132 
  Verifying        : systemd-libs-252.16-1.amzn2023.0.1.aarch64          72/132 
  Verifying        : libfdisk-2.37.4-1.amzn2023.0.3.aarch64              73/132 
  Verifying        : libstdc++-11.4.1-2.amzn2023.0.2.aarch64             74/132 
  Verifying        : which-2.21-26.amzn2023.0.2.aarch64                  75/132 
  Verifying        : libtasn1-4.19.0-1.amzn2023.0.4.aarch64              76/132 
  Verifying        : file-libs-5.39-7.amzn2023.0.4.aarch64               77/132 
  Verifying        : zip-3.0-28.amzn2023.0.2.aarch64                     78/132 
  Verifying        : lz4-libs-1.9.4-1.amzn2023.0.2.aarch64               79/132 
  Verifying        : p11-kit-0.24.1-2.amzn2023.0.3.aarch64               80/132 
  Verifying        : libssh-0.10.5-1.amzn2023.0.2.aarch64                81/132 
  Verifying        : sqlite-libs-3.40.0-1.amzn2023.0.3.aarch64           82/132 
  Verifying        : libcap-ng-0.8.2-4.amzn2023.0.2.aarch64              83/132 
  Verifying        : libattr-2.5.1-3.amzn2023.0.2.aarch64                84/132 
  Verifying        : sed-4.8-7.amzn2023.0.2.aarch64                      85/132 
  Verifying        : openldap-2.4.57-6.amzn2023.0.6.aarch64              86/132 
  Verifying        : gdb-minimal-12.1-5.amzn2023.0.3.aarch64             87/132 
  Verifying        : zstd-1.5.5-1.amzn2023.0.1.aarch64                   88/132 
  Verifying        : rpm-4.16.1.3-12.amzn2023.0.6.aarch64                89/132 
  Verifying        : libsemanage-3.4-5.amzn2023.0.2.aarch64              90/132 
  Verifying        : glibc-2.34-52.amzn2023.0.7.aarch64                  91/132 
  Verifying        : libunistring-0.9.10-10.amzn2023.0.2.aarch64         92/132 
  Verifying        : xxhash-libs-0.8.0-3.amzn2023.0.2.aarch64            93/132 
  Verifying        : libdb-5.3.28-49.amzn2023.0.2.aarch64                94/132 
  Verifying        : pkgconf-1.8.0-4.amzn2023.0.2.aarch64                95/132 
  Verifying        : libcurl-8.3.0-1.amzn2023.0.2.aarch64                96/132 
  Verifying        : libidn2-2.3.2-1.amzn2023.0.5.aarch64                97/132 
  Verifying        : libcom_err-1.46.5-2.amzn2023.0.2.aarch64            98/132 
  Verifying        : bzip2-1.0.8-6.amzn2023.0.2.aarch64                  99/132 
  Verifying        : libarchive-3.5.3-2.amzn2023.0.3.aarch64            100/132 
  Verifying        : gzip-1.12-1.amzn2023.0.1.aarch64                   101/132 
  Verifying        : curl-8.3.0-1.amzn2023.0.2.aarch64                  102/132 
  Verifying        : krb5-libs-1.21-3.amzn2023.0.3.aarch64              103/132 
  Verifying        : libnghttp2-1.57.0-1.amzn2023.0.1.aarch64           104/132 
  Verifying        : libmount-2.37.4-1.amzn2023.0.3.aarch64             105/132 
  Verifying        : xz-libs-5.2.5-9.amzn2023.0.2.aarch64               106/132 
  Verifying        : glibc-gconv-extra-2.34-52.amzn2023.0.7.aarch64     107/132 
  Verifying        : jansson-2.14-0.amzn2023.aarch64                    108/132 
  Verifying        : libgomp-11.4.1-2.amzn2023.0.2.aarch64              109/132 
  Verifying        : libuuid-2.37.4-1.amzn2023.0.3.aarch64              110/132 
  Verifying        : glibc-minimal-langpack-2.34-52.amzn2023.0.7.aarc   111/132 
  Verifying        : libsepol-3.4-3.amzn2023.0.3.aarch64                112/132 
  Verifying        : cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.aarch64      113/132 
  Verifying        : pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.aarch64    114/132 
  Verifying        : libpwquality-1.4.4-6.amzn2023.0.2.aarch64          115/132 
  Verifying        : ed-1.14.2-10.amzn2023.0.2.aarch64                  116/132 
  Verifying        : shadow-utils-2:4.9-12.amzn2023.0.4.aarch64         117/132 
  Verifying        : libgcc-11.4.1-2.amzn2023.0.2.aarch64               118/132 
  Verifying        : gdbm-libs-1:1.19-2.amzn2023.0.2.aarch64            119/132 
  Verifying        : libxcrypt-4.4.33-7.amzn2023.aarch64                120/132 
  Verifying        : binutils-2.39-6.amzn2023.0.10.aarch64              121/132 
  Verifying        : pam-1.5.1-8.amzn2023.0.3.aarch64                   122/132 
  Verifying        : rpm-libs-4.16.1.3-12.amzn2023.0.6.aarch64          123/132 
  Verifying        : grep-3.8-1.amzn2023.0.4.aarch64                    124/132 
  Verifying        : libpsl-0.21.1-3.amzn2023.0.2.aarch64               125/132 
  Verifying        : libxml2-2.10.4-1.amzn2023.0.6.aarch64              126/132 
  Verifying        : alternatives-1.15-2.amzn2023.0.2.aarch64           127/132 
  Verifying        : info-6.7-10.amzn2023.0.2.aarch64                   128/132 
  Verifying        : file-5.39-7.amzn2023.0.4.aarch64                   129/132 
  Verifying        : openssl-libs-1:3.0.8-1.amzn2023.0.10.aarch64       130/132 
  Verifying        : xz-5.2.5-9.amzn2023.0.2.aarch64                    131/132 
  Verifying        : cracklib-2.9.6-27.amzn2023.0.2.aarch64             132/132 

Installed:
  alternatives-1.15-2.amzn2023.0.2.aarch64                                      
  amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023.noarch                       
  amazon-rpm-config-228-3.amzn2023.0.2.noarch                                   
  audit-libs-3.0.6-1.amzn2023.0.2.aarch64                                       
  basesystem-11-11.amzn2023.0.2.noarch                                          
  bash-5.2.15-1.amzn2023.0.2.aarch64                                            
  binutils-2.39-6.amzn2023.0.10.aarch64                                         
  bzip2-1.0.8-6.amzn2023.0.2.aarch64                                            
  bzip2-libs-1.0.8-6.amzn2023.0.2.aarch64                                       
  ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarch                             
  coreutils-8.32-30.amzn2023.0.3.aarch64                                        
  coreutils-common-8.32-30.amzn2023.0.3.aarch64                                 
  cpio-2.13-13.amzn2023.0.2.aarch64                                             
  cracklib-2.9.6-27.amzn2023.0.2.aarch64                                        
  crypto-policies-20220428-1.gitdfb10ea.amzn2023.0.2.noarch                     
  curl-8.3.0-1.amzn2023.0.2.aarch64                                             
  cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.aarch64                                 
  diffutils-3.8-1.amzn2023.0.2.aarch64                                          
  dwz-0.14-6.amzn2023.0.2.aarch64                                               
  ed-1.14.2-10.amzn2023.0.2.aarch64                                             
  efi-srpm-macros-5-4.amzn2023.0.5.noarch                                       
  elfutils-0.188-3.amzn2023.0.2.aarch64                                         
  elfutils-debuginfod-client-0.188-3.amzn2023.0.2.aarch64                       
  elfutils-default-yama-scope-0.188-3.amzn2023.0.2.noarch                       
  elfutils-libelf-0.188-3.amzn2023.0.2.aarch64                                  
  elfutils-libs-0.188-3.amzn2023.0.2.aarch64                                    
  file-5.39-7.amzn2023.0.4.aarch64                                              
  file-libs-5.39-7.amzn2023.0.4.aarch64                                         
  filesystem-3.14-5.amzn2023.0.3.aarch64                                        
  findutils-1:4.8.0-2.amzn2023.0.2.aarch64                                      
  fonts-srpm-macros-1:2.0.5-12.amzn2023.0.2.noarch                              
  gawk-5.1.0-3.amzn2023.0.3.aarch64                                             
  gdb-minimal-12.1-5.amzn2023.0.3.aarch64                                       
  gdbm-libs-1:1.19-2.amzn2023.0.2.aarch64                                       
  ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch                                   
  glibc-2.34-52.amzn2023.0.7.aarch64                                            
  glibc-common-2.34-52.amzn2023.0.7.aarch64                                     
  glibc-gconv-extra-2.34-52.amzn2023.0.7.aarch64                                
  glibc-minimal-langpack-2.34-52.amzn2023.0.7.aarch64                           
  gmp-1:6.2.1-2.amzn2023.0.2.aarch64                                            
  go-srpm-macros-3.3.1-1.amzn2023.noarch                                        
  grep-3.8-1.amzn2023.0.4.aarch64                                               
  gzip-1.12-1.amzn2023.0.1.aarch64                                              
  info-6.7-10.amzn2023.0.2.aarch64                                              
  jansson-2.14-0.amzn2023.aarch64                                               
  kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch                                 
  keyutils-libs-1.6.3-1.amzn2023.aarch64                                        
  krb5-libs-1.21-3.amzn2023.0.3.aarch64                                         
  libacl-2.3.1-2.amzn2023.0.2.aarch64                                           
  libarchive-3.5.3-2.amzn2023.0.3.aarch64                                       
  libattr-2.5.1-3.amzn2023.0.2.aarch64                                          
  libblkid-2.37.4-1.amzn2023.0.3.aarch64                                        
  libbrotli-1.0.9-4.amzn2023.0.2.aarch64                                        
  libcap-2.48-2.amzn2023.0.3.aarch64                                            
  libcap-ng-0.8.2-4.amzn2023.0.2.aarch64                                        
  libcom_err-1.46.5-2.amzn2023.0.2.aarch64                                      
  libcurl-8.3.0-1.amzn2023.0.2.aarch64                                          
  libdb-5.3.28-49.amzn2023.0.2.aarch64                                          
  libeconf-0.4.0-1.amzn2023.0.3.aarch64                                         
  libfdisk-2.37.4-1.amzn2023.0.3.aarch64                                        
  libffi-3.4.4-1.amzn2023.0.1.aarch64                                           
  libgcc-11.4.1-2.amzn2023.0.2.aarch64                                          
  libgomp-11.4.1-2.amzn2023.0.2.aarch64                                         
  libidn2-2.3.2-1.amzn2023.0.5.aarch64                                          
  libmount-2.37.4-1.amzn2023.0.3.aarch64                                        
  libnghttp2-1.57.0-1.amzn2023.0.1.aarch64                                      
  libpkgconf-1.8.0-4.amzn2023.0.2.aarch64                                       
  libpsl-0.21.1-3.amzn2023.0.2.aarch64                                          
  libpwquality-1.4.4-6.amzn2023.0.2.aarch64                                     
  libselinux-3.4-5.amzn2023.0.2.aarch64                                         
  libsemanage-3.4-5.amzn2023.0.2.aarch64                                        
  libsepol-3.4-3.amzn2023.0.3.aarch64                                           
  libsigsegv-2.13-2.amzn2023.0.2.aarch64                                        
  libsmartcols-2.37.4-1.amzn2023.0.3.aarch64                                    
  libssh-0.10.5-1.amzn2023.0.2.aarch64                                          
  libssh-config-0.10.5-1.amzn2023.0.2.noarch                                    
  libstdc++-11.4.1-2.amzn2023.0.2.aarch64                                       
  libtasn1-4.19.0-1.amzn2023.0.4.aarch64                                        
  libunistring-0.9.10-10.amzn2023.0.2.aarch64                                   
  libutempter-1.2.1-4.amzn2023.0.2.aarch64                                      
  libuuid-2.37.4-1.amzn2023.0.3.aarch64                                         
  libverto-0.3.2-1.amzn2023.0.2.aarch64                                         
  libxcrypt-4.4.33-7.amzn2023.aarch64                                           
  libxml2-2.10.4-1.amzn2023.0.6.aarch64                                         
  libzstd-1.5.5-1.amzn2023.0.1.aarch64                                          
  lua-libs-5.4.4-3.amzn2023.0.2.aarch64                                         
  lua-srpm-macros-1-4.amzn2023.0.2.noarch                                       
  lz4-libs-1.9.4-1.amzn2023.0.2.aarch64                                         
  mpfr-4.1.0-7.amzn2023.0.2.aarch64                                             
  ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch                               
  ncurses-libs-6.2-4.20200222.amzn2023.0.4.aarch64                              
  ocaml-srpm-macros-6-6.amzn2023.0.2.noarch                                     
  openblas-srpm-macros-2-9.amzn2023.0.2.noarch                                  
  openldap-2.4.57-6.amzn2023.0.6.aarch64                                        
  openssl-libs-1:3.0.8-1.amzn2023.0.10.aarch64                                  
  p11-kit-0.24.1-2.amzn2023.0.3.aarch64                                         
  p11-kit-trust-0.24.1-2.amzn2023.0.3.aarch64                                   
  package-notes-srpm-macros-0.4-18.amzn2023.0.5.noarch                          
  pam-1.5.1-8.amzn2023.0.3.aarch64                                              
  patch-2.7.6-14.amzn2023.0.2.aarch64                                           
  pcre2-10.40-1.amzn2023.0.3.aarch64                                            
  pcre2-syntax-10.40-1.amzn2023.0.3.noarch                                      
  perl-srpm-macros-1-39.amzn2023.0.2.noarch                                     
  pkgconf-1.8.0-4.amzn2023.0.2.aarch64                                          
  pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch                                        
  pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.aarch64                               
  popt-1.18-6.amzn2023.0.2.aarch64                                              
  publicsuffix-list-dafsa-20221208-60.amzn2023.noarch                           
  python-srpm-macros-3.9-41.amzn2023.0.5.noarch                                 
  readline-8.1-2.amzn2023.0.2.aarch64                                           
  rpm-4.16.1.3-12.amzn2023.0.6.aarch64                                          
  rpm-build-4.16.1.3-12.amzn2023.0.6.aarch64                                    
  rpm-build-libs-4.16.1.3-12.amzn2023.0.6.aarch64                               
  rpm-libs-4.16.1.3-12.amzn2023.0.6.aarch64                                     
  rust-srpm-macros-21-42.amzn2023.0.2.noarch                                    
  sed-4.8-7.amzn2023.0.2.aarch64                                                
  setup-2.13.7-3.amzn2023.0.2.noarch                                            
  shadow-utils-2:4.9-12.amzn2023.0.4.aarch64                                    
  sqlite-libs-3.40.0-1.amzn2023.0.3.aarch64                                     
  system-release-2023.3.20231218-0.amzn2023.noarch                              
  systemd-libs-252.16-1.amzn2023.0.1.aarch64                                    
  tar-2:1.34-1.amzn2023.0.3.aarch64                                             
  unzip-6.0-57.amzn2023.0.2.aarch64                                             
  util-linux-2.37.4-1.amzn2023.0.3.aarch64                                      
  util-linux-core-2.37.4-1.amzn2023.0.3.aarch64                                 
  which-2.21-26.amzn2023.0.2.aarch64                                            
  xxhash-libs-0.8.0-3.amzn2023.0.2.aarch64                                      
  xz-5.2.5-9.amzn2023.0.2.aarch64                                               
  xz-libs-5.2.5-9.amzn2023.0.2.aarch64                                          
  zip-3.0-28.amzn2023.0.2.aarch64                                               
  zlib-1.2.11-33.amzn2023.0.5.aarch64                                           
  zstd-1.5.5-1.amzn2023.0.1.aarch64                                             

Complete!
Finish: installing minimal buildroot with dnf
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.15-2.amzn2023.0.2.aarch64
amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023.noarch
amazon-rpm-config-228-3.amzn2023.0.2.noarch
audit-libs-3.0.6-1.amzn2023.0.2.aarch64
basesystem-11-11.amzn2023.0.2.noarch
bash-5.2.15-1.amzn2023.0.2.aarch64
binutils-2.39-6.amzn2023.0.10.aarch64
bzip2-1.0.8-6.amzn2023.0.2.aarch64
bzip2-libs-1.0.8-6.amzn2023.0.2.aarch64
ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarch
coreutils-8.32-30.amzn2023.0.3.aarch64
coreutils-common-8.32-30.amzn2023.0.3.aarch64
cpio-2.13-13.amzn2023.0.2.aarch64
cracklib-2.9.6-27.amzn2023.0.2.aarch64
crypto-policies-20220428-1.gitdfb10ea.amzn2023.0.2.noarch
curl-8.3.0-1.amzn2023.0.2.aarch64
cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.aarch64
diffutils-3.8-1.amzn2023.0.2.aarch64
dwz-0.14-6.amzn2023.0.2.aarch64
ed-1.14.2-10.amzn2023.0.2.aarch64
efi-srpm-macros-5-4.amzn2023.0.5.noarch
elfutils-0.188-3.amzn2023.0.2.aarch64
elfutils-debuginfod-client-0.188-3.amzn2023.0.2.aarch64
elfutils-default-yama-scope-0.188-3.amzn2023.0.2.noarch
elfutils-libelf-0.188-3.amzn2023.0.2.aarch64
elfutils-libs-0.188-3.amzn2023.0.2.aarch64
file-5.39-7.amzn2023.0.4.aarch64
file-libs-5.39-7.amzn2023.0.4.aarch64
filesystem-3.14-5.amzn2023.0.3.aarch64
findutils-4.8.0-2.amzn2023.0.2.aarch64
fonts-srpm-macros-2.0.5-12.amzn2023.0.2.noarch
gawk-5.1.0-3.amzn2023.0.3.aarch64
gdb-minimal-12.1-5.amzn2023.0.3.aarch64
gdbm-libs-1.19-2.amzn2023.0.2.aarch64
ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch
glibc-2.34-52.amzn2023.0.7.aarch64
glibc-common-2.34-52.amzn2023.0.7.aarch64
glibc-gconv-extra-2.34-52.amzn2023.0.7.aarch64
glibc-minimal-langpack-2.34-52.amzn2023.0.7.aarch64
gmp-6.2.1-2.amzn2023.0.2.aarch64
go-srpm-macros-3.3.1-1.amzn2023.noarch
gpg-pubkey-d832c631-6515c85e
grep-3.8-1.amzn2023.0.4.aarch64
gzip-1.12-1.amzn2023.0.1.aarch64
info-6.7-10.amzn2023.0.2.aarch64
jansson-2.14-0.amzn2023.aarch64
kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch
keyutils-libs-1.6.3-1.amzn2023.aarch64
krb5-libs-1.21-3.amzn2023.0.3.aarch64
libacl-2.3.1-2.amzn2023.0.2.aarch64
libarchive-3.5.3-2.amzn2023.0.3.aarch64
libattr-2.5.1-3.amzn2023.0.2.aarch64
libblkid-2.37.4-1.amzn2023.0.3.aarch64
libbrotli-1.0.9-4.amzn2023.0.2.aarch64
libcap-2.48-2.amzn2023.0.3.aarch64
libcap-ng-0.8.2-4.amzn2023.0.2.aarch64
libcom_err-1.46.5-2.amzn2023.0.2.aarch64
libcurl-8.3.0-1.amzn2023.0.2.aarch64
libdb-5.3.28-49.amzn2023.0.2.aarch64
libeconf-0.4.0-1.amzn2023.0.3.aarch64
libfdisk-2.37.4-1.amzn2023.0.3.aarch64
libffi-3.4.4-1.amzn2023.0.1.aarch64
libgcc-11.4.1-2.amzn2023.0.2.aarch64
libgomp-11.4.1-2.amzn2023.0.2.aarch64
libidn2-2.3.2-1.amzn2023.0.5.aarch64
libmount-2.37.4-1.amzn2023.0.3.aarch64
libnghttp2-1.57.0-1.amzn2023.0.1.aarch64
libpkgconf-1.8.0-4.amzn2023.0.2.aarch64
libpsl-0.21.1-3.amzn2023.0.2.aarch64
libpwquality-1.4.4-6.amzn2023.0.2.aarch64
libselinux-3.4-5.amzn2023.0.2.aarch64
libsemanage-3.4-5.amzn2023.0.2.aarch64
libsepol-3.4-3.amzn2023.0.3.aarch64
libsigsegv-2.13-2.amzn2023.0.2.aarch64
libsmartcols-2.37.4-1.amzn2023.0.3.aarch64
libssh-0.10.5-1.amzn2023.0.2.aarch64
libssh-config-0.10.5-1.amzn2023.0.2.noarch
libstdc++-11.4.1-2.amzn2023.0.2.aarch64
libtasn1-4.19.0-1.amzn2023.0.4.aarch64
libunistring-0.9.10-10.amzn2023.0.2.aarch64
libutempter-1.2.1-4.amzn2023.0.2.aarch64
libuuid-2.37.4-1.amzn2023.0.3.aarch64
libverto-0.3.2-1.amzn2023.0.2.aarch64
libxcrypt-4.4.33-7.amzn2023.aarch64
libxml2-2.10.4-1.amzn2023.0.6.aarch64
libzstd-1.5.5-1.amzn2023.0.1.aarch64
lua-libs-5.4.4-3.amzn2023.0.2.aarch64
lua-srpm-macros-1-4.amzn2023.0.2.noarch
lz4-libs-1.9.4-1.amzn2023.0.2.aarch64
mpfr-4.1.0-7.amzn2023.0.2.aarch64
ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch
ncurses-libs-6.2-4.20200222.amzn2023.0.4.aarch64
ocaml-srpm-macros-6-6.amzn2023.0.2.noarch
openblas-srpm-macros-2-9.amzn2023.0.2.noarch
openldap-2.4.57-6.amzn2023.0.6.aarch64
openssl-libs-3.0.8-1.amzn2023.0.10.aarch64
p11-kit-0.24.1-2.amzn2023.0.3.aarch64
p11-kit-trust-0.24.1-2.amzn2023.0.3.aarch64
package-notes-srpm-macros-0.4-18.amzn2023.0.5.noarch
pam-1.5.1-8.amzn2023.0.3.aarch64
patch-2.7.6-14.amzn2023.0.2.aarch64
pcre2-10.40-1.amzn2023.0.3.aarch64
pcre2-syntax-10.40-1.amzn2023.0.3.noarch
perl-srpm-macros-1-39.amzn2023.0.2.noarch
pkgconf-1.8.0-4.amzn2023.0.2.aarch64
pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch
pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.aarch64
popt-1.18-6.amzn2023.0.2.aarch64
publicsuffix-list-dafsa-20221208-60.amzn2023.noarch
python-srpm-macros-3.9-41.amzn2023.0.5.noarch
readline-8.1-2.amzn2023.0.2.aarch64
rpm-4.16.1.3-12.amzn2023.0.6.aarch64
rpm-build-4.16.1.3-12.amzn2023.0.6.aarch64
rpm-build-libs-4.16.1.3-12.amzn2023.0.6.aarch64
rpm-libs-4.16.1.3-12.amzn2023.0.6.aarch64
rust-srpm-macros-21-42.amzn2023.0.2.noarch
sed-4.8-7.amzn2023.0.2.aarch64
setup-2.13.7-3.amzn2023.0.2.noarch
shadow-utils-4.9-12.amzn2023.0.4.aarch64
sqlite-libs-3.40.0-1.amzn2023.0.3.aarch64
system-release-2023.3.20231218-0.amzn2023.noarch
systemd-libs-252.16-1.amzn2023.0.1.aarch64
tar-1.34-1.amzn2023.0.3.aarch64
unzip-6.0-57.amzn2023.0.2.aarch64
util-linux-2.37.4-1.amzn2023.0.3.aarch64
util-linux-core-2.37.4-1.amzn2023.0.3.aarch64
which-2.21-26.amzn2023.0.2.aarch64
xxhash-libs-0.8.0-3.amzn2023.0.2.aarch64
xz-5.2.5-9.amzn2023.0.2.aarch64
xz-libs-5.2.5-9.amzn2023.0.2.aarch64
zip-3.0-28.amzn2023.0.2.aarch64
zlib-1.2.11-33.amzn2023.0.5.aarch64
zstd-1.5.5-1.amzn2023.0.1.aarch64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1689984000
Wrote: /builddir/build/SRPMS/samtools-1.15.1-3.amzn2023.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/amazonlinux-2023-aarch64-1704591447.273799/root/var/log/dnf.rpm.log
/var/lib/mock/amazonlinux-2023-aarch64-1704591447.273799/root/var/log/dnf.librepo.log
/var/lib/mock/amazonlinux-2023-aarch64-1704591447.273799/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-0k4aumou/samtools/samtools.spec) Config(child) 0 minutes 20 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/samtools-1.15.1-3.amzn2023.src.rpm)  Config(amazonlinux-2023-aarch64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-aarch64-bootstrap-1704591447.273799/root.
INFO: reusing tmpfs at /var/lib/mock/amazonlinux-2023-aarch64-bootstrap-1704591447.273799/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-aarch64-1704591447.273799/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.16.1.3-12.amzn2023.0.6.aarch64
  python3-dnf-4.12.0-2.amzn2023.0.4.noarch
  python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch
  yum-4.12.0-2.amzn2023.0.4.noarch
Finish: chroot init
Start: build phase for samtools-1.15.1-3.amzn2023.src.rpm
Start: build setup for samtools-1.15.1-3.amzn2023.src.rpm
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1689984000
Wrote: /builddir/build/SRPMS/samtools-1.15.1-3.amzn2023.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  46 kB/s | 1.5 kB     00:00    
Amazon Linux 2023 repository - aarch64          9.8 kB/s | 3.6 kB     00:00    
Dependencies resolved.
================================================================================
 Package                Arch    Version                       Repository   Size
================================================================================
Installing:
 gcc                    aarch64 11.4.1-2.amzn2023.0.2         amazonlinux  30 M
 htslib-devel           aarch64 1.15.1-3.amzn2023             copr_base   100 k
 htslib-tools           aarch64 1.15.1-3.amzn2023             copr_base   544 k
 make                   aarch64 1:4.3-5.amzn2023.0.2          amazonlinux 530 k
 ncurses-devel          aarch64 6.2-4.20200222.amzn2023.0.4   amazonlinux 510 k
 perl-FindBin           noarch  1.51-477.amzn2023.0.6         amazonlinux  14 k
 perl-Getopt-Long       noarch  1:2.52-2.amzn2023.0.2         amazonlinux  60 k
 perl-interpreter       aarch64 4:5.32.1-477.amzn2023.0.6     amazonlinux  71 k
 perl-lib               aarch64 0.65-477.amzn2023.0.6         amazonlinux  15 k
 zlib-devel             aarch64 1.2.11-33.amzn2023.0.5        amazonlinux  45 k
Installing dependencies:
 annobin-docs           noarch  10.93-1.amzn2023.0.1          amazonlinux  92 k
 annobin-plugin-gcc     aarch64 10.93-1.amzn2023.0.1          amazonlinux 886 k
 cpp                    aarch64 11.4.1-2.amzn2023.0.2         amazonlinux 9.8 M
 gc                     aarch64 8.0.4-5.amzn2023.0.2          amazonlinux 102 k
 glibc-devel            aarch64 2.34-52.amzn2023.0.7          amazonlinux 455 k
 groff-base             aarch64 1.22.4-7.amzn2023.0.2         amazonlinux 1.0 M
 guile22                aarch64 2.2.7-2.amzn2023.0.3          amazonlinux 6.4 M
 htslib                 aarch64 1.15.1-3.amzn2023             copr_base   484 k
 kernel-headers         aarch64 6.1.66-91.160.amzn2023        amazonlinux 1.4 M
 libasan                aarch64 11.4.1-2.amzn2023.0.2         amazonlinux 401 k
 libatomic              aarch64 11.4.1-2.amzn2023.0.2         amazonlinux  35 k
 libmpc                 aarch64 1.2.1-2.amzn2023.0.2          amazonlinux  63 k
 libtool-ltdl           aarch64 2.4.7-1.amzn2023.0.3          amazonlinux  38 k
 libubsan               aarch64 11.4.1-2.amzn2023.0.2         amazonlinux 183 k
 libxcrypt-devel        aarch64 4.4.33-7.amzn2023             amazonlinux  32 k
 ncurses                aarch64 6.2-4.20200222.amzn2023.0.4   amazonlinux 395 k
 ncurses-c++-libs       aarch64 6.2-4.20200222.amzn2023.0.4   amazonlinux  36 k
 perl-Carp              noarch  1.50-458.amzn2023.0.2         amazonlinux  29 k
 perl-Class-Struct      noarch  0.66-477.amzn2023.0.6         amazonlinux  22 k
 perl-DynaLoader        aarch64 1.47-477.amzn2023.0.6         amazonlinux  26 k
 perl-Encode            aarch64 4:3.15-462.amzn2023.0.2       amazonlinux 1.7 M
 perl-Errno             aarch64 1.30-477.amzn2023.0.6         amazonlinux  15 k
 perl-Exporter          noarch  5.74-459.amzn2023.0.2         amazonlinux  31 k
 perl-Fcntl             aarch64 1.13-477.amzn2023.0.6         amazonlinux  21 k
 perl-File-Basename     noarch  2.85-477.amzn2023.0.6         amazonlinux  18 k
 perl-File-Path         noarch  2.18-2.amzn2023.0.2           amazonlinux  36 k
 perl-File-Temp         noarch  1:0.231.100-2.amzn2023.0.2    amazonlinux  60 k
 perl-File-stat         noarch  1.09-477.amzn2023.0.6         amazonlinux  17 k
 perl-Getopt-Std        noarch  1.12-477.amzn2023.0.6         amazonlinux  16 k
 perl-HTTP-Tiny         noarch  0.078-1.amzn2023.0.3          amazonlinux  56 k
 perl-IO                aarch64 1.43-477.amzn2023.0.6         amazonlinux  87 k
 perl-IPC-Open3         noarch  1.21-477.amzn2023.0.6         amazonlinux  23 k
 perl-MIME-Base64       aarch64 3.16-2.amzn2023.0.2           amazonlinux  31 k
 perl-POSIX             aarch64 1.94-477.amzn2023.0.6         amazonlinux  97 k
 perl-PathTools         aarch64 3.78-459.amzn2023.0.2         amazonlinux  86 k
 perl-Pod-Escapes       noarch  1:1.07-458.amzn2023.0.2       amazonlinux  20 k
 perl-Pod-Perldoc       noarch  3.28.01-459.amzn2023.0.3      amazonlinux  84 k
 perl-Pod-Simple        noarch  1:3.42-2.amzn2023.0.2         amazonlinux 215 k
 perl-Pod-Usage         noarch  4:2.01-2.amzn2023.0.2         amazonlinux  41 k
 perl-Scalar-List-Utils aarch64 4:1.56-459.amzn2023.0.2       amazonlinux  71 k
 perl-SelectSaver       noarch  1.02-477.amzn2023.0.6         amazonlinux  12 k
 perl-Socket            aarch64 4:2.032-1.amzn2023.0.2        amazonlinux  55 k
 perl-Storable          aarch64 1:3.21-458.amzn2023.0.2       amazonlinux  94 k
 perl-Symbol            noarch  1.08-477.amzn2023.0.6         amazonlinux  15 k
 perl-Term-ANSIColor    noarch  5.01-459.amzn2023.0.2         amazonlinux  48 k
 perl-Term-Cap          noarch  1.17-458.amzn2023.0.2         amazonlinux  22 k
 perl-Text-ParseWords   noarch  3.30-458.amzn2023.0.2         amazonlinux  17 k
 perl-Text-Tabs+Wrap    noarch  2021.0726-1.amzn2023.0.1      amazonlinux  22 k
 perl-Time-Local        noarch  2:1.300-5.amzn2023.0.2        amazonlinux  34 k
 perl-constant          noarch  1.33-459.amzn2023.0.2         amazonlinux  23 k
 perl-if                noarch  0.60.800-477.amzn2023.0.6     amazonlinux  14 k
 perl-libs              aarch64 4:5.32.1-477.amzn2023.0.6     amazonlinux 2.0 M
 perl-mro               aarch64 1.23-477.amzn2023.0.6         amazonlinux  28 k
 perl-overload          noarch  1.31-477.amzn2023.0.6         amazonlinux  46 k
 perl-overloading       noarch  0.02-477.amzn2023.0.6         amazonlinux  13 k
 perl-parent            noarch  1:0.238-458.amzn2023.0.2      amazonlinux  14 k
 perl-podlators         noarch  1:4.14-458.amzn2023.0.2       amazonlinux 112 k
 perl-subs              noarch  1.03-477.amzn2023.0.6         amazonlinux  12 k
 perl-vars              noarch  1.05-477.amzn2023.0.6         amazonlinux  13 k

Transaction Summary
================================================================================
Install  69 Packages

Total size: 59 M
Total download size: 1.6 M
Installed size: 199 M
Downloading Packages:
[SKIPPED] perl-podlators-4.14-458.amzn2023.0.2.noarch.rpm: Already downloaded  
[SKIPPED] perl-Carp-1.50-458.amzn2023.0.2.noarch.rpm: Already downloaded       
[SKIPPED] perl-parent-0.238-458.amzn2023.0.2.noarch.rpm: Already downloaded    
[SKIPPED] perl-Time-Local-1.300-5.amzn2023.0.2.noarch.rpm: Already downloaded  
[SKIPPED] perl-constant-1.33-459.amzn2023.0.2.noarch.rpm: Already downloaded   
[SKIPPED] perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch.rpm: Already downloaded
[SKIPPED] perl-FindBin-1.51-477.amzn2023.0.6.noarch.rpm: Already downloaded    
[SKIPPED] perl-File-Temp-0.231.100-2.amzn2023.0.2.noarch.rpm: Already downloaded
[SKIPPED] perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch.rpm: Already downloaded
[SKIPPED] perl-if-0.60.800-477.amzn2023.0.6.noarch.rpm: Already downloaded     
[SKIPPED] perl-Term-Cap-1.17-458.amzn2023.0.2.noarch.rpm: Already downloaded   
[SKIPPED] perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarch.rpm: Already downloaded
[SKIPPED] perl-overloading-0.02-477.amzn2023.0.6.noarch.rpm: Already downloaded
[SKIPPED] perl-Exporter-5.74-459.amzn2023.0.2.noarch.rpm: Already downloaded   
[SKIPPED] perl-File-Basename-2.85-477.amzn2023.0.6.noarch.rpm: Already downloaded
[SKIPPED] perl-subs-1.03-477.amzn2023.0.6.noarch.rpm: Already downloaded       
[SKIPPED] perl-File-stat-1.09-477.amzn2023.0.6.noarch.rpm: Already downloaded  
[SKIPPED] perl-Pod-Simple-3.42-2.amzn2023.0.2.noarch.rpm: Already downloaded   
[SKIPPED] perl-Getopt-Long-2.52-2.amzn2023.0.2.noarch.rpm: Already downloaded  
[SKIPPED] perl-overload-1.31-477.amzn2023.0.6.noarch.rpm: Already downloaded   
[SKIPPED] perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch.rpm: Already downloaded 
[SKIPPED] perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch.rpm: Already downloaded  
[SKIPPED] perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch.rpm: Already downloaded   
[SKIPPED] perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch.rpm: Already downloaded
[SKIPPED] perl-Pod-Usage-2.01-2.amzn2023.0.2.noarch.rpm: Already downloaded    
[SKIPPED] perl-Symbol-1.08-477.amzn2023.0.6.noarch.rpm: Already downloaded     
[SKIPPED] perl-SelectSaver-1.02-477.amzn2023.0.6.noarch.rpm: Already downloaded
[SKIPPED] perl-vars-1.05-477.amzn2023.0.6.noarch.rpm: Already downloaded       
[SKIPPED] annobin-docs-10.93-1.amzn2023.0.1.noarch.rpm: Already downloaded     
[SKIPPED] perl-Pod-Escapes-1.07-458.amzn2023.0.2.noarch.rpm: Already downloaded
[SKIPPED] perl-File-Path-2.18-2.amzn2023.0.2.noarch.rpm: Already downloaded    
[SKIPPED] perl-Class-Struct-0.66-477.amzn2023.0.6.noarch.rpm: Already downloaded
[SKIPPED] ncurses-6.2-4.20200222.amzn2023.0.4.aarch64.rpm: Already downloaded  
[SKIPPED] perl-Scalar-List-Utils-1.56-459.amzn2023.0.2.aarch64.rpm: Already downloaded
[SKIPPED] perl-Socket-2.032-1.amzn2023.0.2.aarch64.rpm: Already downloaded     
[SKIPPED] glibc-devel-2.34-52.amzn2023.0.7.aarch64.rpm: Already downloaded     
[SKIPPED] perl-mro-1.23-477.amzn2023.0.6.aarch64.rpm: Already downloaded       
[SKIPPED] gc-8.0.4-5.amzn2023.0.2.aarch64.rpm: Already downloaded              
[SKIPPED] kernel-headers-6.1.66-91.160.amzn2023.aarch64.rpm: Already downloaded
[SKIPPED] perl-POSIX-1.94-477.amzn2023.0.6.aarch64.rpm: Already downloaded     
[SKIPPED] gcc-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded            
[SKIPPED] libtool-ltdl-2.4.7-1.amzn2023.0.3.aarch64.rpm: Already downloaded    
[SKIPPED] guile22-2.2.7-2.amzn2023.0.3.aarch64.rpm: Already downloaded         
[SKIPPED] perl-Storable-3.21-458.amzn2023.0.2.aarch64.rpm: Already downloaded  
[SKIPPED] perl-libs-5.32.1-477.amzn2023.0.6.aarch64.rpm: Already downloaded    
[SKIPPED] perl-IO-1.43-477.amzn2023.0.6.aarch64.rpm: Already downloaded        
[SKIPPED] libasan-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded        
[SKIPPED] perl-MIME-Base64-3.16-2.amzn2023.0.2.aarch64.rpm: Already downloaded 
[SKIPPED] perl-interpreter-5.32.1-477.amzn2023.0.6.aarch64.rpm: Already downloaded
[SKIPPED] annobin-plugin-gcc-10.93-1.amzn2023.0.1.aarch64.rpm: Already downloaded
[SKIPPED] perl-Fcntl-1.13-477.amzn2023.0.6.aarch64.rpm: Already downloaded     
[SKIPPED] groff-base-1.22.4-7.amzn2023.0.2.aarch64.rpm: Already downloaded     
[SKIPPED] perl-Errno-1.30-477.amzn2023.0.6.aarch64.rpm: Already downloaded     
[SKIPPED] perl-DynaLoader-1.47-477.amzn2023.0.6.aarch64.rpm: Already downloaded
[SKIPPED] libubsan-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded       
[SKIPPED] libatomic-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded      
[SKIPPED] libxcrypt-devel-4.4.33-7.amzn2023.aarch64.rpm: Already downloaded    
[SKIPPED] cpp-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded            
[SKIPPED] libmpc-1.2.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded          
[SKIPPED] perl-lib-0.65-477.amzn2023.0.6.aarch64.rpm: Already downloaded       
[SKIPPED] perl-Encode-3.15-462.amzn2023.0.2.aarch64.rpm: Already downloaded    
[SKIPPED] zlib-devel-1.2.11-33.amzn2023.0.5.aarch64.rpm: Already downloaded    
[SKIPPED] perl-PathTools-3.78-459.amzn2023.0.2.aarch64.rpm: Already downloaded 
[SKIPPED] make-4.3-5.amzn2023.0.2.aarch64.rpm: Already downloaded              
(65/69): htslib-devel-1.15.1-3.amzn2023.aarch64 2.3 MB/s | 100 kB     00:00    
(66/69): htslib-tools-1.15.1-3.amzn2023.aarch64  11 MB/s | 544 kB     00:00    
(67/69): htslib-1.15.1-3.amzn2023.aarch64.rpm   8.4 MB/s | 484 kB     00:00    
(68/69): ncurses-c++-libs-6.2-4.20200222.amzn20 2.7 MB/s |  36 kB     00:00    
(69/69): ncurses-devel-6.2-4.20200222.amzn2023.  24 MB/s | 510 kB     00:00    
--------------------------------------------------------------------------------
Total                                           4.0 MB/s | 1.6 MB     00:00     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Installing       : libmpc-1.2.1-2.amzn2023.0.2.aarch64                   1/69 
  Installing       : htslib-1.15.1-3.amzn2023.aarch64                      2/69 
  Installing       : cpp-11.4.1-2.amzn2023.0.2.aarch64                     3/69 
  Installing       : libatomic-11.4.1-2.amzn2023.0.2.aarch64               4/69 
  Installing       : libubsan-11.4.1-2.amzn2023.0.2.aarch64                5/69 
  Installing       : ncurses-c++-libs-6.2-4.20200222.amzn2023.0.4.aarch    6/69 
  Running scriptlet: groff-base-1.22.4-7.amzn2023.0.2.aarch64              7/69 
  Installing       : groff-base-1.22.4-7.amzn2023.0.2.aarch64              7/69 
  Running scriptlet: groff-base-1.22.4-7.amzn2023.0.2.aarch64              7/69 
  Installing       : libasan-11.4.1-2.amzn2023.0.2.aarch64                 8/69 
  Installing       : libtool-ltdl-2.4.7-1.amzn2023.0.3.aarch64             9/69 
  Installing       : kernel-headers-6.1.66-91.160.amzn2023.aarch64        10/69 
  Installing       : libxcrypt-devel-4.4.33-7.amzn2023.aarch64            11/69 
  Installing       : glibc-devel-2.34-52.amzn2023.0.7.aarch64             12/69 
  Installing       : gc-8.0.4-5.amzn2023.0.2.aarch64                      13/69 
  Installing       : guile22-2.2.7-2.amzn2023.0.3.aarch64                 14/69 
  Installing       : make-1:4.3-5.amzn2023.0.2.aarch64                    15/69 
  Installing       : gcc-11.4.1-2.amzn2023.0.2.aarch64                    16/69 
  Running scriptlet: gcc-11.4.1-2.amzn2023.0.2.aarch64                    16/69 
  Installing       : ncurses-6.2-4.20200222.amzn2023.0.4.aarch64          17/69 
  Installing       : perl-if-0.60.800-477.amzn2023.0.6.noarch             18/69 
  Installing       : perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarc   19/69 
  Installing       : perl-Time-Local-2:1.300-5.amzn2023.0.2.noarch        20/69 
  Installing       : perl-Pod-Escapes-1:1.07-458.amzn2023.0.2.noarch      21/69 
  Installing       : perl-File-Path-2.18-2.amzn2023.0.2.noarch            22/69 
  Installing       : perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch     23/69 
  Installing       : perl-subs-1.03-477.amzn2023.0.6.noarch               24/69 
  Installing       : perl-Term-Cap-1.17-458.amzn2023.0.2.noarch           25/69 
  Installing       : perl-Class-Struct-0.66-477.amzn2023.0.6.noarch       26/69 
  Installing       : perl-POSIX-1.94-477.amzn2023.0.6.aarch64             27/69 
  Installing       : perl-Pod-Simple-1:3.42-2.amzn2023.0.2.noarch         28/69 
  Installing       : perl-File-Temp-1:0.231.100-2.amzn2023.0.2.noarch     29/69 
  Installing       : perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch          30/69 
  Installing       : perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch           31/69 
  Installing       : perl-Symbol-1.08-477.amzn2023.0.6.noarch             32/69 
  Installing       : perl-SelectSaver-1.02-477.amzn2023.0.6.noarch        33/69 
  Installing       : perl-Socket-4:2.032-1.amzn2023.0.2.aarch64           34/69 
  Installing       : perl-File-stat-1.09-477.amzn2023.0.6.noarch          35/69 
  Installing       : perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch     36/69 
  Installing       : perl-podlators-1:4.14-458.amzn2023.0.2.noarch        37/69 
  Installing       : perl-overloading-0.02-477.amzn2023.0.6.noarch        38/69 
  Installing       : perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch    39/69 
  Installing       : perl-mro-1.23-477.amzn2023.0.6.aarch64               40/69 
  Installing       : perl-Fcntl-1.13-477.amzn2023.0.6.aarch64             41/69 
  Installing       : perl-IO-1.43-477.amzn2023.0.6.aarch64                42/69 
  Installing       : perl-Pod-Usage-4:2.01-2.amzn2023.0.2.noarch          43/69 
  Installing       : perl-parent-1:0.238-458.amzn2023.0.2.noarch          44/69 
  Installing       : perl-constant-1.33-459.amzn2023.0.2.noarch           45/69 
  Installing       : perl-File-Basename-2.85-477.amzn2023.0.6.noarch      46/69 
  Installing       : perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch         47/69 
  Installing       : perl-vars-1.05-477.amzn2023.0.6.noarch               48/69 
  Installing       : perl-Scalar-List-Utils-4:1.56-459.amzn2023.0.2.aar   49/69 
  Installing       : perl-overload-1.31-477.amzn2023.0.6.noarch           50/69 
  Installing       : perl-MIME-Base64-3.16-2.amzn2023.0.2.aarch64         51/69 
  Installing       : perl-Errno-1.30-477.amzn2023.0.6.aarch64             52/69 
  Installing       : perl-Storable-1:3.21-458.amzn2023.0.2.aarch64        53/69 
  Installing       : perl-Getopt-Long-1:2.52-2.amzn2023.0.2.noarch        54/69 
  Installing       : perl-Carp-1.50-458.amzn2023.0.2.noarch               55/69 
  Installing       : perl-Exporter-5.74-459.amzn2023.0.2.noarch           56/69 
  Installing       : perl-DynaLoader-1.47-477.amzn2023.0.6.aarch64        57/69 
  Installing       : perl-PathTools-3.78-459.amzn2023.0.2.aarch64         58/69 
  Installing       : perl-Encode-4:3.15-462.amzn2023.0.2.aarch64          59/69 
  Installing       : perl-libs-4:5.32.1-477.amzn2023.0.6.aarch64          60/69 
  Installing       : perl-interpreter-4:5.32.1-477.amzn2023.0.6.aarch64   61/69 
  Installing       : annobin-docs-10.93-1.amzn2023.0.1.noarch             62/69 
  Installing       : annobin-plugin-gcc-10.93-1.amzn2023.0.1.aarch64      63/69 
  Running scriptlet: annobin-plugin-gcc-10.93-1.amzn2023.0.1.aarch64      63/69 
  Installing       : perl-FindBin-1.51-477.amzn2023.0.6.noarch            64/69 
  Installing       : perl-lib-0.65-477.amzn2023.0.6.aarch64               65/69 
  Installing       : ncurses-devel-6.2-4.20200222.amzn2023.0.4.aarch64    66/69 
  Installing       : htslib-devel-1.15.1-3.amzn2023.aarch64               67/69 
  Installing       : htslib-tools-1.15.1-3.amzn2023.aarch64               68/69 
  Installing       : zlib-devel-1.2.11-33.amzn2023.0.5.aarch64            69/69 
  Running scriptlet: zlib-devel-1.2.11-33.amzn2023.0.5.aarch64            69/69 
  Verifying        : htslib-1.15.1-3.amzn2023.aarch64                      1/69 
  Verifying        : htslib-devel-1.15.1-3.amzn2023.aarch64                2/69 
  Verifying        : htslib-tools-1.15.1-3.amzn2023.aarch64                3/69 
  Verifying        : perl-podlators-1:4.14-458.amzn2023.0.2.noarch         4/69 
  Verifying        : perl-Carp-1.50-458.amzn2023.0.2.noarch                5/69 
  Verifying        : perl-parent-1:0.238-458.amzn2023.0.2.noarch           6/69 
  Verifying        : perl-Time-Local-2:1.300-5.amzn2023.0.2.noarch         7/69 
  Verifying        : perl-constant-1.33-459.amzn2023.0.2.noarch            8/69 
  Verifying        : perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch     9/69 
  Verifying        : perl-FindBin-1.51-477.amzn2023.0.6.noarch            10/69 
  Verifying        : perl-File-Temp-1:0.231.100-2.amzn2023.0.2.noarch     11/69 
  Verifying        : perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch     12/69 
  Verifying        : perl-if-0.60.800-477.amzn2023.0.6.noarch             13/69 
  Verifying        : perl-Term-Cap-1.17-458.amzn2023.0.2.noarch           14/69 
  Verifying        : perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarc   15/69 
  Verifying        : perl-overloading-0.02-477.amzn2023.0.6.noarch        16/69 
  Verifying        : perl-Exporter-5.74-459.amzn2023.0.2.noarch           17/69 
  Verifying        : perl-File-Basename-2.85-477.amzn2023.0.6.noarch      18/69 
  Verifying        : perl-subs-1.03-477.amzn2023.0.6.noarch               19/69 
  Verifying        : perl-File-stat-1.09-477.amzn2023.0.6.noarch          20/69 
  Verifying        : perl-Pod-Simple-1:3.42-2.amzn2023.0.2.noarch         21/69 
  Verifying        : perl-Getopt-Long-1:2.52-2.amzn2023.0.2.noarch        22/69 
  Verifying        : perl-overload-1.31-477.amzn2023.0.6.noarch           23/69 
  Verifying        : perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch         24/69 
  Verifying        : perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch          25/69 
  Verifying        : perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch           26/69 
  Verifying        : perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch     27/69 
  Verifying        : perl-Pod-Usage-4:2.01-2.amzn2023.0.2.noarch          28/69 
  Verifying        : perl-Symbol-1.08-477.amzn2023.0.6.noarch             29/69 
  Verifying        : perl-SelectSaver-1.02-477.amzn2023.0.6.noarch        30/69 
  Verifying        : perl-vars-1.05-477.amzn2023.0.6.noarch               31/69 
  Verifying        : annobin-docs-10.93-1.amzn2023.0.1.noarch             32/69 
  Verifying        : perl-Pod-Escapes-1:1.07-458.amzn2023.0.2.noarch      33/69 
  Verifying        : perl-File-Path-2.18-2.amzn2023.0.2.noarch            34/69 
  Verifying        : perl-Class-Struct-0.66-477.amzn2023.0.6.noarch       35/69 
  Verifying        : ncurses-6.2-4.20200222.amzn2023.0.4.aarch64          36/69 
  Verifying        : perl-Scalar-List-Utils-4:1.56-459.amzn2023.0.2.aar   37/69 
  Verifying        : perl-Socket-4:2.032-1.amzn2023.0.2.aarch64           38/69 
  Verifying        : glibc-devel-2.34-52.amzn2023.0.7.aarch64             39/69 
  Verifying        : perl-mro-1.23-477.amzn2023.0.6.aarch64               40/69 
  Verifying        : gc-8.0.4-5.amzn2023.0.2.aarch64                      41/69 
  Verifying        : kernel-headers-6.1.66-91.160.amzn2023.aarch64        42/69 
  Verifying        : perl-POSIX-1.94-477.amzn2023.0.6.aarch64             43/69 
  Verifying        : gcc-11.4.1-2.amzn2023.0.2.aarch64                    44/69 
  Verifying        : libtool-ltdl-2.4.7-1.amzn2023.0.3.aarch64            45/69 
  Verifying        : guile22-2.2.7-2.amzn2023.0.3.aarch64                 46/69 
  Verifying        : ncurses-devel-6.2-4.20200222.amzn2023.0.4.aarch64    47/69 
  Verifying        : perl-Storable-1:3.21-458.amzn2023.0.2.aarch64        48/69 
  Verifying        : perl-libs-4:5.32.1-477.amzn2023.0.6.aarch64          49/69 
  Verifying        : perl-IO-1.43-477.amzn2023.0.6.aarch64                50/69 
  Verifying        : libasan-11.4.1-2.amzn2023.0.2.aarch64                51/69 
  Verifying        : perl-MIME-Base64-3.16-2.amzn2023.0.2.aarch64         52/69 
  Verifying        : perl-interpreter-4:5.32.1-477.amzn2023.0.6.aarch64   53/69 
  Verifying        : annobin-plugin-gcc-10.93-1.amzn2023.0.1.aarch64      54/69 
  Verifying        : perl-Fcntl-1.13-477.amzn2023.0.6.aarch64             55/69 
  Verifying        : groff-base-1.22.4-7.amzn2023.0.2.aarch64             56/69 
  Verifying        : perl-Errno-1.30-477.amzn2023.0.6.aarch64             57/69 
  Verifying        : ncurses-c++-libs-6.2-4.20200222.amzn2023.0.4.aarch   58/69 
  Verifying        : perl-DynaLoader-1.47-477.amzn2023.0.6.aarch64        59/69 
  Verifying        : libubsan-11.4.1-2.amzn2023.0.2.aarch64               60/69 
  Verifying        : libatomic-11.4.1-2.amzn2023.0.2.aarch64              61/69 
  Verifying        : libxcrypt-devel-4.4.33-7.amzn2023.aarch64            62/69 
  Verifying        : cpp-11.4.1-2.amzn2023.0.2.aarch64                    63/69 
  Verifying        : libmpc-1.2.1-2.amzn2023.0.2.aarch64                  64/69 
  Verifying        : perl-lib-0.65-477.amzn2023.0.6.aarch64               65/69 
  Verifying        : perl-Encode-4:3.15-462.amzn2023.0.2.aarch64          66/69 
  Verifying        : zlib-devel-1.2.11-33.amzn2023.0.5.aarch64            67/69 
  Verifying        : perl-PathTools-3.78-459.amzn2023.0.2.aarch64         68/69 
  Verifying        : make-1:4.3-5.amzn2023.0.2.aarch64                    69/69 

Installed:
  annobin-docs-10.93-1.amzn2023.0.1.noarch                                      
  annobin-plugin-gcc-10.93-1.amzn2023.0.1.aarch64                               
  cpp-11.4.1-2.amzn2023.0.2.aarch64                                             
  gc-8.0.4-5.amzn2023.0.2.aarch64                                               
  gcc-11.4.1-2.amzn2023.0.2.aarch64                                             
  glibc-devel-2.34-52.amzn2023.0.7.aarch64                                      
  groff-base-1.22.4-7.amzn2023.0.2.aarch64                                      
  guile22-2.2.7-2.amzn2023.0.3.aarch64                                          
  htslib-1.15.1-3.amzn2023.aarch64                                              
  htslib-devel-1.15.1-3.amzn2023.aarch64                                        
  htslib-tools-1.15.1-3.amzn2023.aarch64                                        
  kernel-headers-6.1.66-91.160.amzn2023.aarch64                                 
  libasan-11.4.1-2.amzn2023.0.2.aarch64                                         
  libatomic-11.4.1-2.amzn2023.0.2.aarch64                                       
  libmpc-1.2.1-2.amzn2023.0.2.aarch64                                           
  libtool-ltdl-2.4.7-1.amzn2023.0.3.aarch64                                     
  libubsan-11.4.1-2.amzn2023.0.2.aarch64                                        
  libxcrypt-devel-4.4.33-7.amzn2023.aarch64                                     
  make-1:4.3-5.amzn2023.0.2.aarch64                                             
  ncurses-6.2-4.20200222.amzn2023.0.4.aarch64                                   
  ncurses-c++-libs-6.2-4.20200222.amzn2023.0.4.aarch64                          
  ncurses-devel-6.2-4.20200222.amzn2023.0.4.aarch64                             
  perl-Carp-1.50-458.amzn2023.0.2.noarch                                        
  perl-Class-Struct-0.66-477.amzn2023.0.6.noarch                                
  perl-DynaLoader-1.47-477.amzn2023.0.6.aarch64                                 
  perl-Encode-4:3.15-462.amzn2023.0.2.aarch64                                   
  perl-Errno-1.30-477.amzn2023.0.6.aarch64                                      
  perl-Exporter-5.74-459.amzn2023.0.2.noarch                                    
  perl-Fcntl-1.13-477.amzn2023.0.6.aarch64                                      
  perl-File-Basename-2.85-477.amzn2023.0.6.noarch                               
  perl-File-Path-2.18-2.amzn2023.0.2.noarch                                     
  perl-File-Temp-1:0.231.100-2.amzn2023.0.2.noarch                              
  perl-File-stat-1.09-477.amzn2023.0.6.noarch                                   
  perl-FindBin-1.51-477.amzn2023.0.6.noarch                                     
  perl-Getopt-Long-1:2.52-2.amzn2023.0.2.noarch                                 
  perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch                                  
  perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch                                    
  perl-IO-1.43-477.amzn2023.0.6.aarch64                                         
  perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch                                   
  perl-MIME-Base64-3.16-2.amzn2023.0.2.aarch64                                  
  perl-POSIX-1.94-477.amzn2023.0.6.aarch64                                      
  perl-PathTools-3.78-459.amzn2023.0.2.aarch64                                  
  perl-Pod-Escapes-1:1.07-458.amzn2023.0.2.noarch                               
  perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch                              
  perl-Pod-Simple-1:3.42-2.amzn2023.0.2.noarch                                  
  perl-Pod-Usage-4:2.01-2.amzn2023.0.2.noarch                                   
  perl-Scalar-List-Utils-4:1.56-459.amzn2023.0.2.aarch64                        
  perl-SelectSaver-1.02-477.amzn2023.0.6.noarch                                 
  perl-Socket-4:2.032-1.amzn2023.0.2.aarch64                                    
  perl-Storable-1:3.21-458.amzn2023.0.2.aarch64                                 
  perl-Symbol-1.08-477.amzn2023.0.6.noarch                                      
  perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch                              
  perl-Term-Cap-1.17-458.amzn2023.0.2.noarch                                    
  perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch                             
  perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarch                           
  perl-Time-Local-2:1.300-5.amzn2023.0.2.noarch                                 
  perl-constant-1.33-459.amzn2023.0.2.noarch                                    
  perl-if-0.60.800-477.amzn2023.0.6.noarch                                      
  perl-interpreter-4:5.32.1-477.amzn2023.0.6.aarch64                            
  perl-lib-0.65-477.amzn2023.0.6.aarch64                                        
  perl-libs-4:5.32.1-477.amzn2023.0.6.aarch64                                   
  perl-mro-1.23-477.amzn2023.0.6.aarch64                                        
  perl-overload-1.31-477.amzn2023.0.6.noarch                                    
  perl-overloading-0.02-477.amzn2023.0.6.noarch                                 
  perl-parent-1:0.238-458.amzn2023.0.2.noarch                                   
  perl-podlators-1:4.14-458.amzn2023.0.2.noarch                                 
  perl-subs-1.03-477.amzn2023.0.6.noarch                                        
  perl-vars-1.05-477.amzn2023.0.6.noarch                                        
  zlib-devel-1.2.11-33.amzn2023.0.5.aarch64                                     

Complete!
Finish: build setup for samtools-1.15.1-3.amzn2023.src.rpm
Start: rpmbuild samtools-1.15.1-3.amzn2023.src.rpm
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1689984000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.sKIqOw
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf samtools-1.15.1
+ /usr/bin/bzip2 -dc /builddir/build/SOURCES/samtools-1.15.1.tar.bz2
+ /usr/bin/tar -xof -
+ 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.hs8owe
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -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-1.15.1-3.amzn2023.aarch64.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 1.15.1-3.amzn2023 aarch64
+ cd samtools-1.15.1
+ CFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -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-1.15.1-3.amzn2023.aarch64.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	2024-01-07 01:37:59.174997414 +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=aarch64-amazon-linux-gnu --host=aarch64-amazon-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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -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-1.15.1-3.amzn2023.aarch64.ld' --prefix=/usr --with-htslib=system
checking for gawk... gawk
checking for aarch64-amazon-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 -j4 V=1 VERBOSE=1
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_aux.o bam_aux.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_index.o bam_index.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam.o bam.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_cat.o bam_cat.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_fastq.o bam_fastq.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_plbuf.o bam_plbuf.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_md.o bam_md.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_plcmd.o bam_plcmd.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_reheader.o bam_reheader.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o sam_view.o sam_view.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_rmdup.o bam_rmdup.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_rmdupse.o bam_rmdupse.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -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-1.15.1-3.amzn2023.aarch64.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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_mate.o bam_mate.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_stat.o bam_stat.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam2bcf.o bam2bcf.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o cut_target.o cut_target.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o sample.o sample.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o coverage.o coverage.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam2depth.o bam2depth.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o phase.o phase.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o padding.o padding.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o faidx.o faidx.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bedcov.o bedcov.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o dict.o dict.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o stats_isize.o stats_isize.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bamshuf.o bamshuf.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_flags.o bam_flags.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_sort.o bam_sort.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_split.o bam_split.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_tview.o bam_tview.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_tview_curses.o bam_tview_curses.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_tview_html.o bam_tview_html.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_quickcheck.o bam_quickcheck.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_lpileup.o bam_lpileup.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_addrprg.o bam_addrprg.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o tmp_file.o tmp_file.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o stats.o stats.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_import.o bam_import.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_ampliconclip.o bam_ampliconclip.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_samples.o bam_samples.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o consensus_pileup.o consensus_pileup.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_markdup.o bam_markdup.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o sam_opts.o sam_opts.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o amplicon_stats.o amplicon_stats.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o sam_utils.o sam_utils.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bam_consensus.o bam_consensus.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -DMAQ_LONGREADS -I.  -I./lz4  -c -o misc/maq2sam-long.o misc/maq2sam.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o misc/maq2sam-short.o misc/maq2sam.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bedidx.o bedidx.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o misc/ace2sam.o misc/ace2sam.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o misc/md5sum-lite.o misc/md5sum-lite.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o misc/md5fa.o misc/md5fa.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/test.o test/test.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o misc/wgsim.o misc/wgsim.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o lz4/lz4.o lz4/lz4.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o bamtk.o bamtk.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-1.15.1-3.amzn2023.aarch64.ld -o misc/maq2sam-long misc/maq2sam-long.o -lz 
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I.  -I./lz4  -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.aarch64.ld -o misc/md5sum-lite misc/md5sum-lite.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-1.15.1-3.amzn2023.aarch64.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-1.15.1-3.amzn2023.aarch64.ld -o misc/ace2sam misc/ace2sam.o -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.aarch64.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-1.15.1-3.amzn2023.aarch64.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-1.15.1-3.amzn2023.aarch64.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-1.15.1-3.amzn2023.aarch64.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-1.15.1-3.amzn2023.aarch64.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-1.15.1-3.amzn2023.aarch64.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-1.15.1-3.amzn2023.aarch64.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-1.15.1-3.amzn2023.aarch64.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-1.15.1-3.amzn2023.aarch64.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-1.15.1-3.amzn2023.aarch64.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-1.15.1-3.amzn2023.aarch64.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
lto-wrapper: warning: using serial compilation of 8 LTRANS jobs
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.XKcVSX
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64
++ dirname /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64
+ CFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -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-1.15.1-3.amzn2023.aarch64.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-1.15.1-3.amzn2023.aarch64 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/share/man/man1
/usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/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-1.15.1-3.amzn2023.aarch64/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-1.15.1-3.amzn2023.aarch64/usr/bin
/usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/share/man/man1
++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/zoom2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/blast2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/bowtie2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/export2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/fasta-sanitize.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/interpolate_sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/novo2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/plot-ampliconstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/plot-bamstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/psl2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/sam2vcf.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/samtools.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/seq_cache_populate.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/soap2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/wgsim_eval.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/zoom2sam.pl
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.15.1-3.amzn2023 --unique-debug-suffix -1.15.1-3.amzn2023.aarch64 --unique-debug-src-base samtools-1.15.1-3.amzn2023.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.15.1
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/ace2sam
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/maq2sam-short
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/md5fa
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/maq2sam-long
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/md5fa
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/maq2sam-short
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/ace2sam
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/maq2sam-long
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/samtools
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/md5sum-lite
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/wgsim
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/samtools
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/md5sum-lite
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/bin/wgsim
original debug info size: 2096kB, size after compression: 1892kB
/usr/lib/rpm/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-python-bytecompile '' 0 1
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.HOEAVW
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -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-1.15.1-3.amzn2023.aarch64.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 1.15.1-3.amzn2023 aarch64
+ cd samtools-1.15.1
+ ldd samtools
+ grep -E '/lib(64)?/libhts\.so\.'
	libhts.so.3 => /lib64/libhts.so.3 (0x0000ffff94282000)
+ 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/6v3NakMmW6/bgzip.dat.gz
.. ok

bgzip -c -b 979200 -s 6 /tmp/6v3NakMmW6/bgzip.dat.gz
.. ok

bgzip -c -b 652804 -s 6 /tmp/6v3NakMmW6/bgzip.dat.gz
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/6v3NakMmW6/faidx.fa 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/6v3NakMmW6/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/6v3NakMmW6/faidx.fa 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/6v3NakMmW6/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/6v3NakMmW6/faidx.fa 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/6v3NakMmW6/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/6v3NakMmW6/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/6v3NakMmW6/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/6v3NakMmW6/fqidx.fq 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/6v3NakMmW6/fqidx.fq.gz 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/6v3NakMmW6/fqidx.fq 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/6v3NakMmW6/fqidx.fq.gz 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/6v3NakMmW6/fqidx.fq 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/6v3NakMmW6/fqidx.fq.gz 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/6v3NakMmW6/fqidx.fq 1:99998-100007
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools view /tmp/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/auto_indexed.csi && cat /tmp/6v3NakMmW6/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/6v3NakMmW6/auto_indexed.crai && cat /tmp/6v3NakMmW6/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/6v3NakMmW6/auto_indexed.csi && cat /tmp/6v3NakMmW6/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/6v3NakMmW6/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/auto_indexed.csi && cat /tmp/6v3NakMmW6/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/6v3NakMmW6/auto_indexed.crai && cat /tmp/6v3NakMmW6/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/6v3NakMmW6/auto_indexed.csi && cat /tmp/6v3NakMmW6/auto_indexed.csi
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/6v3NakMmW6/mpileup.bam.list -f /tmp/6v3NakMmW6/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/6v3NakMmW6/mpileup.cram.list -f /tmp/6v3NakMmW6/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/6v3NakMmW6/mpileup.bam.urllist -f /tmp/6v3NakMmW6/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/6v3NakMmW6/mpileup.cram.urllist -f /tmp/6v3NakMmW6/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/6v3NakMmW6/mpileup.ref.fa.gz -r17:1050-1060 /tmp/6v3NakMmW6/mpileup.1.bam | grep -v mpileup
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/6v3NakMmW6/mpileup.ref.fa.gz -r17:1050-1060 /tmp/6v3NakMmW6/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/6v3NakMmW6/view.001.fogn (SAM input)     .. ok

	50: Count -R /tmp/6v3NakMmW6/view.001.fogn (SAM input)      .. ok

	51: Filter -R /tmp/6v3NakMmW6/view.001.fogn (BAM input)     .. ok

	52: Count -R /tmp/6v3NakMmW6/view.001.fogn (BAM input)      .. ok

	53: Filter -R /tmp/6v3NakMmW6/view.001.fogn (CRAM input)    .. ok

	54: Count -R /tmp/6v3NakMmW6/view.001.fogn (CRAM input)     .. ok

	55: Filter -R /tmp/6v3NakMmW6/view.001.fogn -r grp2 (SAM input).. ok

	56: Count -R /tmp/6v3NakMmW6/view.001.fogn -r grp2 (SAM input).. ok

	57: Filter -R /tmp/6v3NakMmW6/view.001.fogn -r grp2 (BAM input).. ok

	58: Count -R /tmp/6v3NakMmW6/view.001.fogn -r grp2 (BAM input).. ok

	59: Filter -R /tmp/6v3NakMmW6/view.001.fogn -r grp2 (CRAM input).. ok

	60: Count -R /tmp/6v3NakMmW6/view.001.fogn -r grp2 (CRAM input).. ok

	61: Filter -r grp2 -R /tmp/6v3NakMmW6/view.001.fogn (SAM input).. ok

	62: Count -r grp2 -R /tmp/6v3NakMmW6/view.001.fogn (SAM input).. ok

	63: Filter -r grp2 -R /tmp/6v3NakMmW6/view.001.fogn (BAM input).. ok

	64: Count -r grp2 -R /tmp/6v3NakMmW6/view.001.fogn (BAM input).. ok

	65: Filter -r grp2 -R /tmp/6v3NakMmW6/view.001.fogn (CRAM input).. ok

	66: Count -r grp2 -R /tmp/6v3NakMmW6/view.001.fogn (CRAM input).. ok

	67: Filter -N /tmp/6v3NakMmW6/view.001.forn (SAM input)     .. ok

	68: Count -N /tmp/6v3NakMmW6/view.001.forn (SAM input)      .. ok

	69: Filter -N /tmp/6v3NakMmW6/view.001.forn (BAM input)     .. ok

	70: Count -N /tmp/6v3NakMmW6/view.001.forn (BAM input)      .. ok

	71: Filter -N /tmp/6v3NakMmW6/view.001.forn (CRAM input)    .. ok

	72: Count -N /tmp/6v3NakMmW6/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/6v3NakMmW6/view.001.fobc (SAM input)  .. ok

	86: Count -D BC:/tmp/6v3NakMmW6/view.001.fobc (SAM input)   .. ok

	87: Filter -D BC:/tmp/6v3NakMmW6/view.001.fobc (BAM input)  .. ok

	88: Count -D BC:/tmp/6v3NakMmW6/view.001.fobc (BAM input)   .. ok

	89: Filter -D BC:/tmp/6v3NakMmW6/view.001.fobc (CRAM input) .. ok

	90: Count -D BC:/tmp/6v3NakMmW6/view.001.fobc (CRAM input)  .. ok

	91: Filter -D BC:/tmp/6v3NakMmW6/view.001.fobc -d BC:TGCA (SAM input).. ok

	92: Count -D BC:/tmp/6v3NakMmW6/view.001.fobc -d BC:TGCA (SAM input).. ok

	93: Filter -D BC:/tmp/6v3NakMmW6/view.001.fobc -d BC:TGCA (BAM input).. ok

	94: Count -D BC:/tmp/6v3NakMmW6/view.001.fobc -d BC:TGCA (BAM input).. ok

	95: Filter -D BC:/tmp/6v3NakMmW6/view.001.fobc -d BC:TGCA (CRAM input).. ok

	96: Count -D BC:/tmp/6v3NakMmW6/view.001.fobc -d BC:TGCA (CRAM input).. ok

	97: Filter -d BC:TGCA -D BC:/tmp/6v3NakMmW6/view.001.fobc (SAM input).. ok

	98: Count -d BC:TGCA -D BC:/tmp/6v3NakMmW6/view.001.fobc (SAM input).. ok

	99: Filter -d BC:TGCA -D BC:/tmp/6v3NakMmW6/view.001.fobc (BAM input).. ok

	100: Count -d BC:TGCA -D BC:/tmp/6v3NakMmW6/view.001.fobc (BAM input).. ok

	101: Filter -d BC:TGCA -D BC:/tmp/6v3NakMmW6/view.001.fobc (CRAM input).. ok

	102: Count -d BC:TGCA -D BC:/tmp/6v3NakMmW6/view.001.fobc (CRAM input).. ok

	103: Filter -D RG:/tmp/6v3NakMmW6/view.001.fogn (SAM input) .. ok

	104: Count -D RG:/tmp/6v3NakMmW6/view.001.fogn (SAM input)  .. ok

	105: Filter -D RG:/tmp/6v3NakMmW6/view.001.fogn (BAM input) .. ok

	106: Count -D RG:/tmp/6v3NakMmW6/view.001.fogn (BAM input)  .. ok

	107: Filter -D RG:/tmp/6v3NakMmW6/view.001.fogn (CRAM input).. ok

	108: Count -D RG:/tmp/6v3NakMmW6/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/6v3NakMmW6/view.test115.sam -h -d TGCA /tmp/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/view.test117.sam -h -d TGCA /tmp/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/view.test119.sam -h -d TGCA /tmp/6v3NakMmW6/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/6v3NakMmW6/view.test006.cram --no-PG


.. expected failure

	121: Filter -D BClong:/tmp/6v3NakMmW6/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/6v3NakMmW6/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/6v3NakMmW6/view.test121.sam -h -D BClong:/tmp/6v3NakMmW6/view.001.fobc /tmp/6v3NakMmW6/view.001.sam --no-PG


.. expected failure

	122: Count -D BClong:/tmp/6v3NakMmW6/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/6v3NakMmW6/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/6v3NakMmW6/view.001.fobc /tmp/6v3NakMmW6/view.001.sam --no-PG


.. expected failure

	123: Filter -D BClong:/tmp/6v3NakMmW6/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/6v3NakMmW6/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/6v3NakMmW6/view.test123.sam -h -D BClong:/tmp/6v3NakMmW6/view.001.fobc /tmp/6v3NakMmW6/view.test001.bam --no-PG


.. expected failure

	124: Count -D BClong:/tmp/6v3NakMmW6/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/6v3NakMmW6/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/6v3NakMmW6/view.001.fobc /tmp/6v3NakMmW6/view.test001.bam --no-PG


.. expected failure

	125: Filter -D BClong:/tmp/6v3NakMmW6/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/6v3NakMmW6/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/6v3NakMmW6/view.test125.sam -h -D BClong:/tmp/6v3NakMmW6/view.001.fobc /tmp/6v3NakMmW6/view.test006.cram --no-PG


.. expected failure

	126: Count -D BClong:/tmp/6v3NakMmW6/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/6v3NakMmW6/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/6v3NakMmW6/view.001.fobc /tmp/6v3NakMmW6/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/6v3NakMmW6/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/bam2fq.discard.s.fq -0 /tmp/6v3NakMmW6/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/6v3NakMmW6/bam2fq.discard.s.fq -0 /tmp/6v3NakMmW6/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/PmRs2b3hEo - /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/6v3NakMmW6/merge.tag.1.bam /tmp/6v3NakMmW6/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/6v3NakMmW6/merge.tag.3.bam /tmp/6v3NakMmW6/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/6v3NakMmW6/merge.bed.1.bam /tmp/6v3NakMmW6/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/xyLzunFv3m - /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/6v3NakMmW6/merge.tag.1.bam /tmp/6v3NakMmW6/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/6v3NakMmW6/merge.tag.3.bam /tmp/6v3NakMmW6/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/6v3NakMmW6/merge.bed.1.bam /tmp/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /tmp/6v3NakMmW6/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/6v3NakMmW6/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/6v3NakMmW6/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-1.15.1-3.amzn2023.aarch64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.yRu8ZM
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ DOCDIR=/builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/share/doc/samtools
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/share/doc/samtools
+ cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/share/doc/samtools
+ cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/share/doc/samtools
+ cp -pr NEWS /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/share/doc/samtools
+ cp -pr examples/ /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/share/doc/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.TbhtoG
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/share/licenses/samtools
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/share/licenses/samtools
+ cp -pr LICENSE /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64/usr/share/licenses/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: samtools = 1.15.1-3.amzn2023 samtools(aarch-64) = 1.15.1-3.amzn2023
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: samtools-debugsource-1.15.1-3.amzn2023.aarch64
Provides: samtools-debugsource = 1.15.1-3.amzn2023 samtools-debugsource(aarch-64) = 1.15.1-3.amzn2023
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: samtools-debuginfo-1.15.1-3.amzn2023.aarch64
Provides: debuginfo(build-id) = 06c55071ee93b20ba56fe700c8cfc4921064f922 debuginfo(build-id) = 2875eb5eb4007217bcbaf5554d71cc5049704fcc debuginfo(build-id) = 4dfbd07cd6662d5dcbc89f4c7b1d754b91ee2c61 debuginfo(build-id) = 64d5f33a009b362dd75ad768cb06f6d9a610d77c debuginfo(build-id) = 7efe0e5ea5219bfb56513141730c831d74fc3456 debuginfo(build-id) = b576a75bdea1c8cdf1307ba88c2d0db090611383 debuginfo(build-id) = c1eb2fb7954a055c075142d099fcdad1b9153e04 samtools-debuginfo = 1.15.1-3.amzn2023 samtools-debuginfo(aarch-64) = 1.15.1-3.amzn2023
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: samtools-debugsource(aarch-64) = 1.15.1-3.amzn2023
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64
Wrote: /builddir/build/RPMS/samtools-1.15.1-3.amzn2023.aarch64.rpm
Wrote: /builddir/build/RPMS/samtools-debugsource-1.15.1-3.amzn2023.aarch64.rpm
Wrote: /builddir/build/RPMS/samtools-debuginfo-1.15.1-3.amzn2023.aarch64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.BVgUOV
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.aarch64
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild samtools-1.15.1-3.amzn2023.src.rpm
Finish: build phase for samtools-1.15.1-3.amzn2023.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/amazonlinux-2023-aarch64-1704591447.273799/root/var/log/dnf.rpm.log
/var/lib/mock/amazonlinux-2023-aarch64-1704591447.273799/root/var/log/dnf.librepo.log
/var/lib/mock/amazonlinux-2023-aarch64-1704591447.273799/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/samtools-1.15.1-3.amzn2023.src.rpm) Config(child) 1 minutes 5 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "samtools",
            "epoch": null,
            "version": "1.15.1",
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RPMResults finished