0s autopkgtest [17:11:38]: starting date and time: 2024-03-16 17:11:38+0000 0s autopkgtest [17:11:38]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:11:38]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ke_17fll/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib,src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl --apt-upgrade htslib --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=htslib/1.19+ds-1.1build2 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-2.secgroup --name adt-noble-arm64-htslib-20240316-171138-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 73s autopkgtest [17:12:51]: testbed dpkg architecture: arm64 74s autopkgtest [17:12:52]: testbed apt version: 2.7.12 74s autopkgtest [17:12:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 74s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 75s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 75s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 75s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 75s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 75s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 75s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 75s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 75s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 75s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 76s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 76s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 76s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 77s Fetched 9063 kB in 2s (4481 kB/s) 78s Reading package lists... 81s Reading package lists... 82s Building dependency tree... 82s Reading state information... 83s Calculating upgrade... 84s The following packages will be REMOVED: 84s libssl3 84s The following NEW packages will be installed: 84s libssl3t64 84s The following packages have been kept back: 84s curl 84s The following packages will be upgraded: 84s openssl ubuntu-minimal ubuntu-standard 84s 3 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 84s Need to get 2775 kB of archives. 84s After this operation, 72.7 kB of additional disk space will be used. 84s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 84s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 84s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 84s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 86s Fetched 2775 kB in 1s (3979 kB/s) 86s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 86s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 86s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 87s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 87s wget depends on libssl3 (>= 3.0.0). 87s u-boot-tools depends on libssl3 (>= 3.0.0). 87s tnftp depends on libssl3 (>= 3.0.0). 87s tcpdump depends on libssl3 (>= 3.0.0). 87s systemd-resolved depends on libssl3 (>= 3.0.0). 87s systemd depends on libssl3 (>= 3.0.0). 87s sudo depends on libssl3 (>= 3.0.0). 87s sbsigntool depends on libssl3 (>= 3.0.0). 87s rsync depends on libssl3 (>= 3.0.0). 87s python3-cryptography depends on libssl3 (>= 3.0.0). 87s openssh-server depends on libssl3 (>= 3.0.10). 87s openssh-client depends on libssl3 (>= 3.0.10). 87s mtd-utils depends on libssl3 (>= 3.0.0). 87s mokutil depends on libssl3 (>= 3.0.0). 87s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 87s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 87s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 87s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 87s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 87s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 87s libnvme1 depends on libssl3 (>= 3.0.0). 87s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 87s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 87s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 87s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 87s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 87s kmod depends on libssl3 (>= 3.0.0). 87s dhcpcd-base depends on libssl3 (>= 3.0.0). 87s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 87s 87s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 87s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 87s Selecting previously unselected package libssl3t64:arm64. 87s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74747 files and directories currently installed.) 87s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 87s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 87s Preparing to unpack .../ubuntu-minimal_1.536_arm64.deb ... 87s Unpacking ubuntu-minimal (1.536) over (1.535) ... 87s Preparing to unpack .../ubuntu-standard_1.536_arm64.deb ... 87s Unpacking ubuntu-standard (1.536) over (1.535) ... 87s Setting up ubuntu-minimal (1.536) ... 87s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 87s Setting up ubuntu-standard (1.536) ... 87s Setting up openssl (3.0.13-0ubuntu1) ... 87s Processing triggers for man-db (2.12.0-3) ... 88s Processing triggers for libc-bin (2.39-0ubuntu2) ... 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 91s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 91s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 91s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 91s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 93s Reading package lists... 93s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s Calculating upgrade... 96s The following packages have been kept back: 96s curl 96s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 98s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 101s autopkgtest [17:13:19]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 101s autopkgtest [17:13:19]: @@@@@@@@@@@@@@@@@@@@ apt-source htslib 105s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe htslib 1.19+ds-1.1build2 (dsc) [2584 B] 105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe htslib 1.19+ds-1.1build2 (tar) [1522 kB] 105s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe htslib 1.19+ds-1.1build2 (diff) [21.4 kB] 106s gpgv: Signature made Sat Mar 16 06:59:33 2024 UTC 106s gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D 106s gpgv: issuer "steve.langasek@ubuntu.com" 106s gpgv: Can't check signature: No public key 106s dpkg-source: warning: cannot verify inline signature for ./htslib_1.19+ds-1.1build2.dsc: no acceptable signature found 108s autopkgtest [17:13:26]: testing package htslib version 1.19+ds-1.1build2 108s autopkgtest [17:13:26]: build not needed 110s autopkgtest [17:13:28]: test run-unit-test: preparing testbed 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Starting pkgProblemResolver with broken count: 1 113s Starting 2 pkgProblemResolver with broken count: 1 113s Investigating (0) autopkgtest-satdep:arm64 < none -> 0 @un puN Ib > 113s Broken autopkgtest-satdep:arm64 Depends on libhts3t64:arm64 < none | 1.19+ds-1.1build2 @un uH > 113s Considering libhts3t64:arm64 1 as a solution to autopkgtest-satdep:arm64 9998 113s Re-Instated libnettle8t64:arm64 113s Re-Instated libhogweed6t64:arm64 113s Re-Instated libgnutls30t64:arm64 113s Re-Instated libpsl5t64:arm64 113s Re-Instated libcurl3t64-gnutls:arm64 113s Re-Instated libdeflate0:arm64 113s Re-Instated libhtscodecs2:arm64 113s Re-Instated libhts3t64:arm64 113s Broken autopkgtest-satdep:arm64 Depends on libhts-dev:arm64 < none | 1.19+ds-1.1build2 @un uH > 113s Considering libhts-dev:arm64 1 as a solution to autopkgtest-satdep:arm64 9998 113s Re-Instated libcurl4-gnutls-dev:arm64 113s Re-Instated libdeflate-dev:arm64 113s Re-Instated liblzma-dev:arm64 113s Re-Instated libc-dev-bin:arm64 113s Re-Instated linux-libc-dev:arm64 113s Re-Instated libcrypt-dev:arm64 113s Re-Instated libtirpc-dev:arm64 113s Re-Instated libnsl-dev:arm64 113s Re-Instated rpcsvc-proto:arm64 113s Re-Instated libc6-dev:arm64 113s Re-Instated zlib1g-dev:arm64 113s Re-Instated libhts-dev:arm64 113s Broken autopkgtest-satdep:arm64 Depends on htslib-test:arm64 < none | 1.19+ds-1.1build2 @un uH > 113s Considering htslib-test:arm64 1 as a solution to autopkgtest-satdep:arm64 9998 113s Re-Instated htslib-test:arm64 113s Broken autopkgtest-satdep:arm64 Depends on tabix:arm64 < none | 1.19+ds-1.1build2 @un uH > 113s Considering tabix:arm64 1 as a solution to autopkgtest-satdep:arm64 9998 113s Re-Instated tabix:arm64 113s Broken autopkgtest-satdep:arm64 Depends on build-essential:arm64 < none | 12.10ubuntu1 @un umH > 113s Considering build-essential:arm64 3 as a solution to autopkgtest-satdep:arm64 9998 113s Re-Instated libisl23:arm64 113s Re-Instated libmpc3:arm64 113s Re-Instated cpp-13-aarch64-linux-gnu:arm64 113s Re-Instated cpp-13:arm64 113s Re-Instated cpp-aarch64-linux-gnu:arm64 113s Re-Instated cpp:arm64 113s Re-Instated libcc1-0:arm64 113s Re-Instated libgomp1:arm64 113s Re-Instated libitm1:arm64 113s Re-Instated libatomic1:arm64 113s Re-Instated libasan8:arm64 113s Re-Instated liblsan0:arm64 113s Re-Instated libtsan2:arm64 113s Re-Instated libubsan1:arm64 113s Re-Instated libhwasan0:arm64 113s Re-Instated libgcc-13-dev:arm64 113s Re-Instated gcc-13-aarch64-linux-gnu:arm64 113s Re-Instated gcc-13:arm64 113s Re-Instated gcc-aarch64-linux-gnu:arm64 113s Re-Instated gcc:arm64 113s Re-Instated libstdc++-13-dev:arm64 113s Re-Instated g++-13-aarch64-linux-gnu:arm64 113s Re-Instated g++-13:arm64 113s Re-Instated g++-aarch64-linux-gnu:arm64 113s Re-Instated g++:arm64 113s Re-Instated build-essential:arm64 113s Broken autopkgtest-satdep:arm64 Depends on dpkg-dev:arm64 < 1.22.4ubuntu5 @ii mK > (>= 1.22.5) 113s Considering dpkg-dev:arm64 0 as a solution to autopkgtest-satdep:arm64 9998 113s Broken autopkgtest-satdep:arm64 Depends on debhelper-compat:arm64 < none @un H > (= 13) 113s Considering debhelper:arm64 0 as a solution to autopkgtest-satdep:arm64 9998 113s Re-Instated autotools-dev:arm64 113s Re-Instated m4:arm64 113s Re-Instated autoconf:arm64 113s Re-Instated automake:arm64 113s Re-Instated autopoint:arm64 113s Re-Instated libdebhelper-perl:arm64 113s Re-Instated libtool:arm64 113s Re-Instated dh-autoreconf:arm64 113s Re-Instated libarchive-zip-perl:arm64 113s Re-Instated libsub-override-perl:arm64 113s Re-Instated libfile-stripnondeterminism-perl:arm64 113s Re-Instated dh-strip-nondeterminism:arm64 113s Re-Instated libdw1:arm64 113s Re-Instated debugedit:arm64 113s Re-Instated dwz:arm64 113s Re-Instated gettext:arm64 113s Re-Instated intltool-debian:arm64 113s Re-Instated po-debconf:arm64 113s Re-Instated debhelper:arm64 113s Broken autopkgtest-satdep:arm64 Depends on libbz2-dev:arm64 < none | 1.0.8-5ubuntu1 @un uH > 113s Considering libbz2-dev:arm64 1 as a solution to autopkgtest-satdep:arm64 9998 113s Re-Instated libbz2-dev:arm64 113s Broken autopkgtest-satdep:arm64 Depends on libssl-dev:arm64 < none | 3.0.13-0ubuntu1 @un uH > 113s Considering libssl-dev:arm64 1 as a solution to autopkgtest-satdep:arm64 9998 113s Re-Instated libssl-dev:arm64 113s Broken autopkgtest-satdep:arm64 Depends on libhtscodecs-dev:arm64 < none | 1.6.0-1 @un uH > (>= 1.0) 113s Considering libhtscodecs-dev:arm64 0 as a solution to autopkgtest-satdep:arm64 9998 113s Re-Instated libhtscodecs-dev:arm64 113s Investigating (0) libgnutls30t64:arm64 < none -> 3.8.3-1.1ubuntu2 @un uN Ib > 113s Broken libgnutls30t64:arm64 Breaks on libgnutls30:arm64 < 3.8.3-1ubuntu1 @ii mK > (< 3.8.3-1.1ubuntu2) 113s Considering libgnutls30:arm64 132 as a solution to libgnutls30t64:arm64 0 113s Holding Back libgnutls30t64:arm64 rather than change libgnutls30:arm64 113s Investigating (0) libhogweed6t64:arm64 < none -> 3.9.1-2.2 @un uN Ib > 113s Broken libhogweed6t64:arm64 Breaks on libhogweed6:arm64 < 3.9.1-2 @ii mK > (< 3.9.1-2.2) 113s Considering libhogweed6:arm64 21 as a solution to libhogweed6t64:arm64 0 113s Holding Back libhogweed6t64:arm64 rather than change libhogweed6:arm64 113s Investigating (0) libpsl5t64:arm64 < none -> 0.21.2-1.1 @un uN Ib > 113s Broken libpsl5t64:arm64 Breaks on libpsl5:arm64 < 0.21.2-1build1 @ii mK > (< 0.21.2-1.1) 113s Considering libpsl5:arm64 12 as a solution to libpsl5t64:arm64 0 113s Holding Back libpsl5t64:arm64 rather than change libpsl5:arm64 113s Investigating (0) libnettle8t64:arm64 < none -> 3.9.1-2.2 @un uN Ib > 113s Broken libnettle8t64:arm64 Breaks on libnettle8:arm64 < 3.9.1-2 @ii mK > (< 3.9.1-2.2) 113s Considering libnettle8:arm64 30 as a solution to libnettle8t64:arm64 0 113s Holding Back libnettle8t64:arm64 rather than change libnettle8:arm64 113s Investigating (0) libcurl3t64-gnutls:arm64 < none -> 8.5.0-2ubuntu7 @un uN Ib > 113s Broken libcurl3t64-gnutls:arm64 Depends on libgnutls30t64:arm64 < none | 3.8.3-1.1ubuntu2 @un uH > (>= 3.8.2) 113s Considering libgnutls30t64:arm64 0 as a solution to libcurl3t64-gnutls:arm64 0 113s Holding Back libcurl3t64-gnutls:arm64 rather than change libgnutls30t64:arm64 113s Investigating (1) autopkgtest-satdep:arm64 < none -> 0 @un puN Ib > 113s Broken autopkgtest-satdep:arm64 Depends on dpkg-dev:arm64 < 1.22.4ubuntu5 @ii mK > (>= 1.22.5) 113s Considering dpkg-dev:arm64 0 as a solution to autopkgtest-satdep:arm64 9998 113s Investigating (1) libcurl4-gnutls-dev:arm64 < none -> 8.5.0-2ubuntu7 @un uN Ib > 113s Broken libcurl4-gnutls-dev:arm64 Depends on libcurl3t64-gnutls:arm64 < none | 8.5.0-2ubuntu7 @un uH > (= 8.5.0-2ubuntu7) 113s Considering libcurl3t64-gnutls:arm64 0 as a solution to libcurl4-gnutls-dev:arm64 1 113s Holding Back libcurl4-gnutls-dev:arm64 rather than change libcurl3t64-gnutls:arm64 113s Investigating (1) libhts-dev:arm64 < none -> 1.19+ds-1.1build2 @un uN Ib > 113s Broken libhts-dev:arm64 Depends on libcurl4-gnutls-dev:arm64 < none | 8.5.0-2ubuntu7 @un uH > 113s Considering libcurl4-gnutls-dev:arm64 1 as a solution to libhts-dev:arm64 1 113s Holding Back libhts-dev:arm64 rather than change libcurl4-gnutls-dev:arm64 113s Investigating (1) libhts3t64:arm64 < none -> 1.19+ds-1.1build2 @un uN Ib > 113s Broken libhts3t64:arm64 Depends on libcurl3t64-gnutls:arm64 < none | 8.5.0-2ubuntu7 @un uH > (>= 7.18.0) 113s Considering libcurl3t64-gnutls:arm64 0 as a solution to libhts3t64:arm64 1 113s Holding Back libhts3t64:arm64 rather than change libcurl3t64-gnutls:arm64 113s Investigating (2) autopkgtest-satdep:arm64 < none -> 0 @un puN Ib > 113s Broken autopkgtest-satdep:arm64 Depends on libhts3t64:arm64 < none | 1.19+ds-1.1build2 @un uH > 113s Considering libhts3t64:arm64 1 as a solution to autopkgtest-satdep:arm64 9998 113s Broken autopkgtest-satdep:arm64 Depends on libhts-dev:arm64 < none | 1.19+ds-1.1build2 @un uH > 113s Considering libhts-dev:arm64 1 as a solution to autopkgtest-satdep:arm64 9998 113s Considering libhts-dev:arm64 1 as a solution to autopkgtest-satdep:arm64 9998 113s Broken autopkgtest-satdep:arm64 Depends on dpkg-dev:arm64 < 1.22.4ubuntu5 @ii mK > (>= 1.22.5) 113s Considering dpkg-dev:arm64 0 as a solution to autopkgtest-satdep:arm64 9998 113s Broken autopkgtest-satdep:arm64 Depends on libcurl4-gnutls-dev:arm64 < none | 8.5.0-2ubuntu7 @un uH > 113s Considering libcurl4-gnutls-dev:arm64 1 as a solution to autopkgtest-satdep:arm64 9998 113s Considering libcurl4-gnutls-dev:arm64 1 as a solution to autopkgtest-satdep:arm64 9998 113s Done 113s Some packages could not be installed. This may mean that you have 113s requested an impossible situation or if you are using the unstable 113s distribution that some required packages have not yet been created 113s or been moved out of Incoming. 113s The following information may help to resolve the situation: 113s 113s The following packages have unmet dependencies: 113s autopkgtest-satdep : Depends: libhts3t64 but it is not going to be installed 113s Depends: libhts-dev but it is not going to be installed 113s Depends: dpkg-dev (>= 1.22.5) but 1.22.4ubuntu5 is to be installed 113s Depends: libcurl4-gnutls-dev but it is not going to be installed 113s E: Unable to correct problems, you have held broken packages. 113s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from noble-proposed 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Starting pkgProblemResolver with broken count: 0 115s Starting 2 pkgProblemResolver with broken count: 0 115s Done 117s The following additional packages will be installed: 117s autoconf automake autopoint autotools-dev build-essential cpp cpp-13 117s cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu curl debhelper debugedit 117s dh-autoreconf dh-strip-nondeterminism dpkg dpkg-dev dwz g++ g++-13 117s g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 117s gcc-13-aarch64-linux-gnu gcc-13-base gcc-14-base gcc-aarch64-linux-gnu 117s gettext htslib-test intltool-debian libarchive-zip-perl libasan8 libatomic1 117s libbz2-dev libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcrypt-dev 117s libcurl3t64-gnutls libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl 117s libdeflate-dev libdeflate0 libdpkg-perl libdw1t64 libelf1t64 117s libfile-stripnondeterminism-perl libgcc-13-dev libgcc-s1 libgnutls30t64 117s libgomp1 libhogweed6t64 libhts-dev libhts3t64 libhtscodecs-dev libhtscodecs2 117s libhwasan0 libisl23 libitm1 liblsan0 liblzma-dev liblzma5 libmpc3 117s libnettle8t64 libpsl5t64 libssl-dev libstdc++-13-dev libstdc++6 117s libsub-override-perl libtool libtsan2 libubsan1 linux-libc-dev locales m4 117s po-debconf rpcsvc-proto tabix xz-utils zlib1g zlib1g-dev 117s Suggested packages: 117s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-13-locales 117s cpp-13-doc dh-make debsig-verify debian-keyring gcc-13-doc gcc-multilib 117s manpages-dev flex bison gdb gcc-doc gdb-aarch64-linux-gnu gettext-doc 117s libasprintf-dev libgettextpo-dev manpages glibc-doc libcurl4-doc 117s libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev 117s libssh2-1-dev pkg-config git bzr gnutls-bin liblzma-doc libssl-doc 117s libstdc++-13-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 117s libmail-box-perl 117s Recommended packages: 117s fakeroot libalgorithm-merge-perl bzip2-doc manpages manpages-dev 117s libc-devtools libfile-fcntllock-perl libarchive-cpio-perl libltdl-dev 117s libmail-sendmail-perl 117s The following packages will be REMOVED: 117s libcurl3-gnutls libcurl4 libelf1 libgnutls30 libhogweed6 libnettle8 libpsl5 117s The following NEW packages will be installed: 117s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 117s cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 117s debugedit dh-autoreconf dh-strip-nondeterminism dwz g++ g++-13 117s g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 117s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext htslib-test 117s intltool-debian libarchive-zip-perl libasan8 libatomic1 libbz2-dev 117s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl3t64-gnutls 117s libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl libdeflate-dev libdeflate0 117s libdw1t64 libelf1t64 libfile-stripnondeterminism-perl libgcc-13-dev 117s libgnutls30t64 libgomp1 libhogweed6t64 libhts-dev libhts3t64 117s libhtscodecs-dev libhtscodecs2 libhwasan0 libisl23 libitm1 liblsan0 117s liblzma-dev libmpc3 libnettle8t64 libpsl5t64 libssl-dev libstdc++-13-dev 117s libsub-override-perl libtool libtsan2 libubsan1 linux-libc-dev m4 po-debconf 117s rpcsvc-proto tabix zlib1g-dev 117s The following packages will be upgraded: 117s curl dpkg dpkg-dev gcc-13-base gcc-14-base libc-bin libc6 libdpkg-perl 117s libgcc-s1 liblzma5 libstdc++6 locales xz-utils zlib1g 117s 14 upgraded, 71 newly installed, 7 to remove and 210 not upgraded. 117s Need to get 94.8 MB/94.8 MB of archives. 117s After this operation, 280 MB of additional disk space will be used. 117s Get:1 /tmp/autopkgtest.T4wPj3/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [828 B] 117s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dpkg arm64 1.22.6ubuntu2 [1265 kB] 118s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-14-base arm64 14-20240315-1ubuntu1 [47.0 kB] 118s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgcc-s1 arm64 14-20240315-1ubuntu1 [49.9 kB] 118s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libstdc++6 arm64 14-20240315-1ubuntu1 [748 kB] 118s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc6 arm64 2.39-0ubuntu6 [2776 kB] 118s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc-bin arm64 2.39-0ubuntu6 [591 kB] 118s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnettle8t64 arm64 3.9.1-2.2 [192 kB] 118s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libhogweed6t64 arm64 3.9.1-2.2 [199 kB] 118s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgnutls30t64 arm64 3.8.3-1.1ubuntu2 [1042 kB] 118s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 118s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 118s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 118s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl3t64-gnutls arm64 8.5.0-2ubuntu7 [327 kB] 118s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 zlib1g arm64 1:1.3.dfsg-3.1ubuntu1 [61.7 kB] 118s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libelf1t64 arm64 0.190-1.1build2 [57.9 kB] 118s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblzma5 arm64 5.6.0-0.2 [129 kB] 118s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13-base arm64 13.2.0-19ubuntu1 [47.8 kB] 118s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 locales all 2.39-0ubuntu6 [4232 kB] 118s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 xz-utils arm64 5.6.0-0.2 [272 kB] 118s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 m4 arm64 1.4.19-4 [240 kB] 118s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 autoconf all 2.71-3 [339 kB] 118s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 autotools-dev all 20220109.1 [44.9 kB] 118s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 118s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 autopoint all 0.21-14ubuntu1 [422 kB] 118s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc-dev-bin arm64 2.39-0ubuntu6 [19.7 kB] 118s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 linux-libc-dev arm64 6.8.0-19.19 [1571 kB] 118s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 118s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 118s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc6-dev arm64 2.39-0ubuntu6 [1596 kB] 118s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 118s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 118s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-19ubuntu1 [10.3 MB] 118s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cpp-13 arm64 13.2.0-19ubuntu1 [1032 B] 118s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 118s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 118s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcc1-0 arm64 14-20240315-1ubuntu1 [44.7 kB] 118s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgomp1 arm64 14-20240315-1ubuntu1 [144 kB] 118s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libitm1 arm64 14-20240315-1ubuntu1 [27.8 kB] 118s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libatomic1 arm64 14-20240315-1ubuntu1 [11.4 kB] 118s Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libasan8 arm64 14-20240315-1ubuntu1 [2919 kB] 118s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblsan0 arm64 14-20240315-1ubuntu1 [1282 kB] 118s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtsan2 arm64 14-20240315-1ubuntu1 [2687 kB] 118s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libubsan1 arm64 14-20240315-1ubuntu1 [1150 kB] 118s Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libhwasan0 arm64 14-20240315-1ubuntu1 [1597 kB] 119s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgcc-13-dev arm64 13.2.0-19ubuntu1 [2464 kB] 119s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-19ubuntu1 [20.1 MB] 119s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13 arm64 13.2.0-19ubuntu1 [467 kB] 119s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 119s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 119s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libstdc++-13-dev arm64 13.2.0-19ubuntu1 [2322 kB] 119s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-19ubuntu1 [11.7 MB] 119s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 g++-13 arm64 13.2.0-19ubuntu1 [14.5 kB] 119s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 119s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 119s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dpkg-dev all 1.22.6ubuntu2 [1074 kB] 119s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdpkg-perl all 1.22.6ubuntu2 [269 kB] 119s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 119s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] 119s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libtool all 2.4.7-7 [166 kB] 119s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 dh-autoreconf all 20 [16.1 kB] 119s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 120s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libsub-override-perl all 0.10-1 [10.0 kB] 120s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] 120s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] 120s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdw1t64 arm64 0.190-1.1build2 [258 kB] 120s Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debugedit arm64 1:5.0-5build1 [45.4 kB] 120s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dwz arm64 0.15-1build5 [113 kB] 120s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 gettext arm64 0.21-14ubuntu1 [846 kB] 120s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 120s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 120s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debhelper all 13.14.1ubuntu5 [869 kB] 120s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 htslib-test all 1.19+ds-1.1build2 [1141 kB] 120s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 120s Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4-gnutls-dev arm64 8.5.0-2ubuntu7 [448 kB] 120s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 120s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate-dev arm64 1.19-1 [51.2 kB] 120s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 120s Get:79 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhts3t64 arm64 1.19+ds-1.1build2 [429 kB] 120s Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblzma-dev arm64 5.6.0-0.2 [180 kB] 120s Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1ubuntu1 [894 kB] 120s Get:82 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhts-dev arm64 1.19+ds-1.1build2 [5879 kB] 120s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs-dev arm64 1.6.0-1 [2975 kB] 120s Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl-dev arm64 3.0.13-0ubuntu1 [2335 kB] 120s Get:85 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 tabix arm64 1.19+ds-1.1build2 [515 kB] 121s Preconfiguring packages ... 121s Fetched 94.8 MB in 3s (30.6 MB/s) 121s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74760 files and directories currently installed.) 121s Preparing to unpack .../dpkg_1.22.6ubuntu2_arm64.deb ... 121s Unpacking dpkg (1.22.6ubuntu2) over (1.22.4ubuntu5) ... 122s Setting up dpkg (1.22.6ubuntu2) ... 122s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74760 files and directories currently installed.) 122s Preparing to unpack .../gcc-14-base_14-20240315-1ubuntu1_arm64.deb ... 122s Unpacking gcc-14-base:arm64 (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 123s Setting up gcc-14-base:arm64 (14-20240315-1ubuntu1) ... 123s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74760 files and directories currently installed.) 123s Preparing to unpack .../libgcc-s1_14-20240315-1ubuntu1_arm64.deb ... 123s Unpacking libgcc-s1:arm64 (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 123s Setting up libgcc-s1:arm64 (14-20240315-1ubuntu1) ... 123s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74760 files and directories currently installed.) 123s Preparing to unpack .../libstdc++6_14-20240315-1ubuntu1_arm64.deb ... 123s Unpacking libstdc++6:arm64 (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 123s Setting up libstdc++6:arm64 (14-20240315-1ubuntu1) ... 123s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74760 files and directories currently installed.) 123s Preparing to unpack .../libc6_2.39-0ubuntu6_arm64.deb ... 123s Unpacking libc6:arm64 (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 123s Setting up libc6:arm64 (2.39-0ubuntu6) ... 124s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74760 files and directories currently installed.) 124s Preparing to unpack .../libc-bin_2.39-0ubuntu6_arm64.deb ... 124s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 124s Setting up libc-bin (2.39-0ubuntu6) ... 124s dpkg: libhogweed6:arm64: dependency problems, but removing anyway as you requested: 124s librtmp1:arm64 depends on libhogweed6. 124s libjcat1:arm64 depends on libhogweed6. 124s libgnutls30:arm64 depends on libhogweed6 (>= 3.6). 124s 124s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74760 files and directories currently installed.) 124s Removing libhogweed6:arm64 (3.9.1-2) ... 124s dpkg: libnettle8:arm64: dependency problems, but removing anyway as you requested: 124s librtmp1:arm64 depends on libnettle8. 124s libgnutls30:arm64 depends on libnettle8 (>= 3.9~). 124s libcurl3-gnutls:arm64 depends on libnettle8. 124s libarchive13:arm64 depends on libnettle8. 124s 124s Removing libnettle8:arm64 (3.9.1-2) ... 124s Selecting previously unselected package libnettle8t64:arm64. 124s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74748 files and directories currently installed.) 124s Preparing to unpack .../libnettle8t64_3.9.1-2.2_arm64.deb ... 124s Unpacking libnettle8t64:arm64 (3.9.1-2.2) ... 124s Selecting previously unselected package libhogweed6t64:arm64. 124s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_arm64.deb ... 124s Unpacking libhogweed6t64:arm64 (3.9.1-2.2) ... 125s dpkg: libgnutls30:arm64: dependency problems, but removing anyway as you requested: 125s u-boot-tools depends on libgnutls30 (>= 3.7.3). 125s librtmp1:arm64 depends on libgnutls30 (>= 3.7.2). 125s libldap2:arm64 depends on libgnutls30 (>= 3.8.2). 125s libjcat1:arm64 depends on libgnutls30 (>= 3.7.3). 125s libcurl3-gnutls:arm64 depends on libgnutls30 (>= 3.8.2). 125s fwupd depends on libgnutls30 (>= 3.7.3). 125s dirmngr depends on libgnutls30 (>= 3.8.1). 125s apt depends on libgnutls30 (>= 3.8.1). 125s 125s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74762 files and directories currently installed.) 125s Removing libgnutls30:arm64 (3.8.3-1ubuntu1) ... 125s Selecting previously unselected package libgnutls30t64:arm64. 125s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74753 files and directories currently installed.) 125s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_arm64.deb ... 125s Unpacking libgnutls30t64:arm64 (3.8.3-1.1ubuntu2) ... 125s dpkg: libcurl4:arm64: dependency problems, but removing anyway as you requested: 125s curl depends on libcurl4 (= 8.5.0-2ubuntu2). 125s 125s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74781 files and directories currently installed.) 125s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 125s Selecting previously unselected package libcurl4t64:arm64. 125s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74776 files and directories currently installed.) 125s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 125s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 125s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 125s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 125s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 125s wget depends on libpsl5 (>= 0.16.0). 125s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 125s 125s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74782 files and directories currently installed.) 125s Removing libpsl5:arm64 (0.21.2-1build1) ... 125s Selecting previously unselected package libpsl5t64:arm64. 125s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74777 files and directories currently installed.) 125s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 125s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 125s dpkg: libcurl3-gnutls:arm64: dependency problems, but removing anyway as you requested: 125s libfwupd2:arm64 depends on libcurl3-gnutls (>= 7.63.0). 125s fwupd depends on libcurl3-gnutls (>= 7.63.0). 125s 125s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74783 files and directories currently installed.) 125s Removing libcurl3-gnutls:arm64 (8.5.0-2ubuntu2) ... 125s Selecting previously unselected package libcurl3t64-gnutls:arm64. 125s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74776 files and directories currently installed.) 125s Preparing to unpack .../libcurl3t64-gnutls_8.5.0-2ubuntu7_arm64.deb ... 125s Unpacking libcurl3t64-gnutls:arm64 (8.5.0-2ubuntu7) ... 126s Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu1_arm64.deb ... 126s Unpacking zlib1g:arm64 (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ... 126s Setting up zlib1g:arm64 (1:1.3.dfsg-3.1ubuntu1) ... 126s dpkg: libelf1:arm64: dependency problems, but removing anyway as you requested: 126s linux-headers-6.8.0-11-generic depends on libelf1 (>= 0.144). 126s libbpf1:arm64 depends on libelf1 (>= 0.144). 126s iproute2 depends on libelf1 (>= 0.131). 126s 126s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74783 files and directories currently installed.) 126s Removing libelf1:arm64 (0.190-1) ... 126s Selecting previously unselected package libelf1t64:arm64. 126s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74778 files and directories currently installed.) 126s Preparing to unpack .../libelf1t64_0.190-1.1build2_arm64.deb ... 126s Unpacking libelf1t64:arm64 (0.190-1.1build2) ... 126s Preparing to unpack .../liblzma5_5.6.0-0.2_arm64.deb ... 126s Unpacking liblzma5:arm64 (5.6.0-0.2) over (5.4.5-0.3) ... 126s Setting up liblzma5:arm64 (5.6.0-0.2) ... 126s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74783 files and directories currently installed.) 126s Preparing to unpack .../00-gcc-13-base_13.2.0-19ubuntu1_arm64.deb ... 126s Unpacking gcc-13-base:arm64 (13.2.0-19ubuntu1) over (13.2.0-17ubuntu2) ... 126s Preparing to unpack .../01-locales_2.39-0ubuntu6_all.deb ... 126s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 126s Preparing to unpack .../02-xz-utils_5.6.0-0.2_arm64.deb ... 126s Unpacking xz-utils (5.6.0-0.2) over (5.4.5-0.3) ... 126s Selecting previously unselected package m4. 126s Preparing to unpack .../03-m4_1.4.19-4_arm64.deb ... 126s Unpacking m4 (1.4.19-4) ... 127s Selecting previously unselected package autoconf. 127s Preparing to unpack .../04-autoconf_2.71-3_all.deb ... 127s Unpacking autoconf (2.71-3) ... 127s Selecting previously unselected package autotools-dev. 127s Preparing to unpack .../05-autotools-dev_20220109.1_all.deb ... 127s Unpacking autotools-dev (20220109.1) ... 127s Selecting previously unselected package automake. 127s Preparing to unpack .../06-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 127s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 127s Selecting previously unselected package autopoint. 127s Preparing to unpack .../07-autopoint_0.21-14ubuntu1_all.deb ... 127s Unpacking autopoint (0.21-14ubuntu1) ... 127s Selecting previously unselected package libc-dev-bin. 127s Preparing to unpack .../08-libc-dev-bin_2.39-0ubuntu6_arm64.deb ... 127s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 127s Selecting previously unselected package linux-libc-dev:arm64. 127s Preparing to unpack .../09-linux-libc-dev_6.8.0-19.19_arm64.deb ... 127s Unpacking linux-libc-dev:arm64 (6.8.0-19.19) ... 127s Selecting previously unselected package libcrypt-dev:arm64. 127s Preparing to unpack .../10-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 127s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 127s Selecting previously unselected package rpcsvc-proto. 127s Preparing to unpack .../11-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 127s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 127s Selecting previously unselected package libc6-dev:arm64. 127s Preparing to unpack .../12-libc6-dev_2.39-0ubuntu6_arm64.deb ... 127s Unpacking libc6-dev:arm64 (2.39-0ubuntu6) ... 127s Selecting previously unselected package libisl23:arm64. 127s Preparing to unpack .../13-libisl23_0.26-3_arm64.deb ... 127s Unpacking libisl23:arm64 (0.26-3) ... 127s Selecting previously unselected package libmpc3:arm64. 127s Preparing to unpack .../14-libmpc3_1.3.1-1_arm64.deb ... 127s Unpacking libmpc3:arm64 (1.3.1-1) ... 127s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 127s Preparing to unpack .../15-cpp-13-aarch64-linux-gnu_13.2.0-19ubuntu1_arm64.deb ... 127s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-19ubuntu1) ... 128s Selecting previously unselected package cpp-13. 128s Preparing to unpack .../16-cpp-13_13.2.0-19ubuntu1_arm64.deb ... 128s Unpacking cpp-13 (13.2.0-19ubuntu1) ... 128s Selecting previously unselected package cpp-aarch64-linux-gnu. 128s Preparing to unpack .../17-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 128s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 128s Selecting previously unselected package cpp. 128s Preparing to unpack .../18-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 128s Unpacking cpp (4:13.2.0-7ubuntu1) ... 128s Selecting previously unselected package libcc1-0:arm64. 128s Preparing to unpack .../19-libcc1-0_14-20240315-1ubuntu1_arm64.deb ... 128s Unpacking libcc1-0:arm64 (14-20240315-1ubuntu1) ... 128s Selecting previously unselected package libgomp1:arm64. 128s Preparing to unpack .../20-libgomp1_14-20240315-1ubuntu1_arm64.deb ... 128s Unpacking libgomp1:arm64 (14-20240315-1ubuntu1) ... 128s Selecting previously unselected package libitm1:arm64. 128s Preparing to unpack .../21-libitm1_14-20240315-1ubuntu1_arm64.deb ... 128s Unpacking libitm1:arm64 (14-20240315-1ubuntu1) ... 128s Selecting previously unselected package libatomic1:arm64. 128s Preparing to unpack .../22-libatomic1_14-20240315-1ubuntu1_arm64.deb ... 128s Unpacking libatomic1:arm64 (14-20240315-1ubuntu1) ... 128s Selecting previously unselected package libasan8:arm64. 128s Preparing to unpack .../23-libasan8_14-20240315-1ubuntu1_arm64.deb ... 128s Unpacking libasan8:arm64 (14-20240315-1ubuntu1) ... 128s Selecting previously unselected package liblsan0:arm64. 128s Preparing to unpack .../24-liblsan0_14-20240315-1ubuntu1_arm64.deb ... 128s Unpacking liblsan0:arm64 (14-20240315-1ubuntu1) ... 129s Selecting previously unselected package libtsan2:arm64. 129s Preparing to unpack .../25-libtsan2_14-20240315-1ubuntu1_arm64.deb ... 129s Unpacking libtsan2:arm64 (14-20240315-1ubuntu1) ... 129s Selecting previously unselected package libubsan1:arm64. 129s Preparing to unpack .../26-libubsan1_14-20240315-1ubuntu1_arm64.deb ... 129s Unpacking libubsan1:arm64 (14-20240315-1ubuntu1) ... 129s Selecting previously unselected package libhwasan0:arm64. 129s Preparing to unpack .../27-libhwasan0_14-20240315-1ubuntu1_arm64.deb ... 129s Unpacking libhwasan0:arm64 (14-20240315-1ubuntu1) ... 129s Selecting previously unselected package libgcc-13-dev:arm64. 129s Preparing to unpack .../28-libgcc-13-dev_13.2.0-19ubuntu1_arm64.deb ... 129s Unpacking libgcc-13-dev:arm64 (13.2.0-19ubuntu1) ... 129s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 129s Preparing to unpack .../29-gcc-13-aarch64-linux-gnu_13.2.0-19ubuntu1_arm64.deb ... 129s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-19ubuntu1) ... 130s Selecting previously unselected package gcc-13. 130s Preparing to unpack .../30-gcc-13_13.2.0-19ubuntu1_arm64.deb ... 130s Unpacking gcc-13 (13.2.0-19ubuntu1) ... 130s Selecting previously unselected package gcc-aarch64-linux-gnu. 130s Preparing to unpack .../31-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 130s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 130s Selecting previously unselected package gcc. 130s Preparing to unpack .../32-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 130s Unpacking gcc (4:13.2.0-7ubuntu1) ... 130s Selecting previously unselected package libstdc++-13-dev:arm64. 130s Preparing to unpack .../33-libstdc++-13-dev_13.2.0-19ubuntu1_arm64.deb ... 130s Unpacking libstdc++-13-dev:arm64 (13.2.0-19ubuntu1) ... 130s Selecting previously unselected package g++-13-aarch64-linux-gnu. 130s Preparing to unpack .../34-g++-13-aarch64-linux-gnu_13.2.0-19ubuntu1_arm64.deb ... 130s Unpacking g++-13-aarch64-linux-gnu (13.2.0-19ubuntu1) ... 130s Selecting previously unselected package g++-13. 130s Preparing to unpack .../35-g++-13_13.2.0-19ubuntu1_arm64.deb ... 130s Unpacking g++-13 (13.2.0-19ubuntu1) ... 131s Selecting previously unselected package g++-aarch64-linux-gnu. 131s Preparing to unpack .../36-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 131s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 131s Selecting previously unselected package g++. 131s Preparing to unpack .../37-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 131s Unpacking g++ (4:13.2.0-7ubuntu1) ... 131s Preparing to unpack .../38-dpkg-dev_1.22.6ubuntu2_all.deb ... 131s Unpacking dpkg-dev (1.22.6ubuntu2) over (1.22.4ubuntu5) ... 131s Preparing to unpack .../39-libdpkg-perl_1.22.6ubuntu2_all.deb ... 131s Unpacking libdpkg-perl (1.22.6ubuntu2) over (1.22.4ubuntu5) ... 131s Selecting previously unselected package build-essential. 131s Preparing to unpack .../40-build-essential_12.10ubuntu1_arm64.deb ... 131s Unpacking build-essential (12.10ubuntu1) ... 131s Selecting previously unselected package libdebhelper-perl. 131s Preparing to unpack .../41-libdebhelper-perl_13.14.1ubuntu5_all.deb ... 131s Unpacking libdebhelper-perl (13.14.1ubuntu5) ... 131s Selecting previously unselected package libtool. 131s Preparing to unpack .../42-libtool_2.4.7-7_all.deb ... 131s Unpacking libtool (2.4.7-7) ... 131s Selecting previously unselected package dh-autoreconf. 131s Preparing to unpack .../43-dh-autoreconf_20_all.deb ... 131s Unpacking dh-autoreconf (20) ... 131s Selecting previously unselected package libarchive-zip-perl. 131s Preparing to unpack .../44-libarchive-zip-perl_1.68-1_all.deb ... 131s Unpacking libarchive-zip-perl (1.68-1) ... 131s Selecting previously unselected package libsub-override-perl. 131s Preparing to unpack .../45-libsub-override-perl_0.10-1_all.deb ... 131s Unpacking libsub-override-perl (0.10-1) ... 131s Selecting previously unselected package libfile-stripnondeterminism-perl. 131s Preparing to unpack .../46-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 131s Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... 132s Selecting previously unselected package dh-strip-nondeterminism. 132s Preparing to unpack .../47-dh-strip-nondeterminism_1.13.1-1_all.deb ... 132s Unpacking dh-strip-nondeterminism (1.13.1-1) ... 132s Selecting previously unselected package libdw1t64:arm64. 132s Preparing to unpack .../48-libdw1t64_0.190-1.1build2_arm64.deb ... 132s Unpacking libdw1t64:arm64 (0.190-1.1build2) ... 132s Selecting previously unselected package debugedit. 132s Preparing to unpack .../49-debugedit_1%3a5.0-5build1_arm64.deb ... 132s Unpacking debugedit (1:5.0-5build1) ... 132s Selecting previously unselected package dwz. 132s Preparing to unpack .../50-dwz_0.15-1build5_arm64.deb ... 132s Unpacking dwz (0.15-1build5) ... 132s Selecting previously unselected package gettext. 132s Preparing to unpack .../51-gettext_0.21-14ubuntu1_arm64.deb ... 132s Unpacking gettext (0.21-14ubuntu1) ... 132s Selecting previously unselected package intltool-debian. 132s Preparing to unpack .../52-intltool-debian_0.35.0+20060710.6_all.deb ... 132s Unpacking intltool-debian (0.35.0+20060710.6) ... 132s Selecting previously unselected package po-debconf. 132s Preparing to unpack .../53-po-debconf_1.0.21+nmu1_all.deb ... 132s Unpacking po-debconf (1.0.21+nmu1) ... 132s Selecting previously unselected package debhelper. 132s Preparing to unpack .../54-debhelper_13.14.1ubuntu5_all.deb ... 132s Unpacking debhelper (13.14.1ubuntu5) ... 132s Selecting previously unselected package htslib-test. 132s Preparing to unpack .../55-htslib-test_1.19+ds-1.1build2_all.deb ... 132s Unpacking htslib-test (1.19+ds-1.1build2) ... 132s Selecting previously unselected package libbz2-dev:arm64. 132s Preparing to unpack .../56-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 132s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 132s Selecting previously unselected package libcurl4-gnutls-dev:arm64. 132s Preparing to unpack .../57-libcurl4-gnutls-dev_8.5.0-2ubuntu7_arm64.deb ... 132s Unpacking libcurl4-gnutls-dev:arm64 (8.5.0-2ubuntu7) ... 132s Selecting previously unselected package libdeflate0:arm64. 132s Preparing to unpack .../58-libdeflate0_1.19-1_arm64.deb ... 132s Unpacking libdeflate0:arm64 (1.19-1) ... 132s Selecting previously unselected package libdeflate-dev:arm64. 132s Preparing to unpack .../59-libdeflate-dev_1.19-1_arm64.deb ... 132s Unpacking libdeflate-dev:arm64 (1.19-1) ... 132s Selecting previously unselected package libhtscodecs2:arm64. 132s Preparing to unpack .../60-libhtscodecs2_1.6.0-1_arm64.deb ... 132s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 133s Selecting previously unselected package libhts3t64:arm64. 133s Preparing to unpack .../61-libhts3t64_1.19+ds-1.1build2_arm64.deb ... 133s Unpacking libhts3t64:arm64 (1.19+ds-1.1build2) ... 133s Selecting previously unselected package liblzma-dev:arm64. 133s Preparing to unpack .../62-liblzma-dev_5.6.0-0.2_arm64.deb ... 133s Unpacking liblzma-dev:arm64 (5.6.0-0.2) ... 133s Selecting previously unselected package zlib1g-dev:arm64. 133s Preparing to unpack .../63-zlib1g-dev_1%3a1.3.dfsg-3.1ubuntu1_arm64.deb ... 133s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3.1ubuntu1) ... 133s Selecting previously unselected package libhts-dev:arm64. 133s Preparing to unpack .../64-libhts-dev_1.19+ds-1.1build2_arm64.deb ... 133s Unpacking libhts-dev:arm64 (1.19+ds-1.1build2) ... 133s Selecting previously unselected package libhtscodecs-dev:arm64. 133s Preparing to unpack .../65-libhtscodecs-dev_1.6.0-1_arm64.deb ... 133s Unpacking libhtscodecs-dev:arm64 (1.6.0-1) ... 133s Selecting previously unselected package libssl-dev:arm64. 133s Preparing to unpack .../66-libssl-dev_3.0.13-0ubuntu1_arm64.deb ... 133s Unpacking libssl-dev:arm64 (3.0.13-0ubuntu1) ... 133s Selecting previously unselected package tabix. 133s Preparing to unpack .../67-tabix_1.19+ds-1.1build2_arm64.deb ... 133s Unpacking tabix (1.19+ds-1.1build2) ... 133s Selecting previously unselected package autopkgtest-satdep. 133s Preparing to unpack .../68-1-autopkgtest-satdep.deb ... 133s Unpacking autopkgtest-satdep (0) ... 133s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 133s Setting up libarchive-zip-perl (1.68-1) ... 133s Setting up htslib-test (1.19+ds-1.1build2) ... 133s Setting up libdebhelper-perl (13.14.1ubuntu5) ... 133s Setting up libpsl5t64:arm64 (0.21.2-1.1) ... 133s Setting up libdeflate0:arm64 (1.19-1) ... 133s Setting up linux-libc-dev:arm64 (6.8.0-19.19) ... 133s Setting up m4 (1.4.19-4) ... 133s Setting up libgomp1:arm64 (14-20240315-1ubuntu1) ... 133s Setting up locales (2.39-0ubuntu6) ... 135s Generating locales (this might take a while)... 139s en_US.UTF-8... done 139s Generation complete. 140s Setting up libelf1t64:arm64 (0.190-1.1build2) ... 140s Setting up libdw1t64:arm64 (0.190-1.1build2) ... 140s Setting up libhtscodecs-dev:arm64 (1.6.0-1) ... 140s Setting up libnettle8t64:arm64 (3.9.1-2.2) ... 140s Setting up autotools-dev (20220109.1) ... 140s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 140s Setting up gcc-13-base:arm64 (13.2.0-19ubuntu1) ... 140s Setting up xz-utils (5.6.0-0.2) ... 140s Setting up libssl-dev:arm64 (3.0.13-0ubuntu1) ... 140s Setting up libmpc3:arm64 (1.3.1-1) ... 140s Setting up libatomic1:arm64 (14-20240315-1ubuntu1) ... 140s Setting up autopoint (0.21-14ubuntu1) ... 140s Setting up libdpkg-perl (1.22.6ubuntu2) ... 140s Setting up autoconf (2.71-3) ... 140s Setting up liblzma-dev:arm64 (5.6.0-0.2) ... 140s Setting up libubsan1:arm64 (14-20240315-1ubuntu1) ... 140s Setting up dwz (0.15-1build5) ... 140s Setting up libhogweed6t64:arm64 (3.9.1-2.2) ... 140s Setting up libhwasan0:arm64 (14-20240315-1ubuntu1) ... 140s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 140s Setting up libasan8:arm64 (14-20240315-1ubuntu1) ... 140s Setting up debugedit (1:5.0-5build1) ... 140s Setting up libsub-override-perl (0.10-1) ... 140s Setting up libtsan2:arm64 (14-20240315-1ubuntu1) ... 140s Setting up libisl23:arm64 (0.26-3) ... 140s Setting up libc-dev-bin (2.39-0ubuntu6) ... 140s Setting up libdeflate-dev:arm64 (1.19-1) ... 140s Setting up tabix (1.19+ds-1.1build2) ... 140s Setting up libcc1-0:arm64 (14-20240315-1ubuntu1) ... 140s Setting up liblsan0:arm64 (14-20240315-1ubuntu1) ... 140s Setting up libitm1:arm64 (14-20240315-1ubuntu1) ... 140s Setting up libgnutls30t64:arm64 (3.8.3-1.1ubuntu2) ... 140s Setting up automake (1:1.16.5-1.3ubuntu1) ... 140s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 140s Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... 140s Setting up gettext (0.21-14ubuntu1) ... 140s Setting up cpp-13-aarch64-linux-gnu (13.2.0-19ubuntu1) ... 140s Setting up libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 140s Setting up libcurl3t64-gnutls:arm64 (8.5.0-2ubuntu7) ... 140s Setting up libcurl4-gnutls-dev:arm64 (8.5.0-2ubuntu7) ... 140s Setting up dpkg-dev (1.22.6ubuntu2) ... 140s Setting up intltool-debian (0.35.0+20060710.6) ... 140s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 140s Setting up dh-strip-nondeterminism (1.13.1-1) ... 140s Setting up libgcc-13-dev:arm64 (13.2.0-19ubuntu1) ... 140s Setting up libhts3t64:arm64 (1.19+ds-1.1build2) ... 140s Setting up libc6-dev:arm64 (2.39-0ubuntu6) ... 140s Setting up curl (8.5.0-2ubuntu7) ... 140s Setting up libstdc++-13-dev:arm64 (13.2.0-19ubuntu1) ... 140s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 140s Setting up cpp-13 (13.2.0-19ubuntu1) ... 140s Setting up po-debconf (1.0.21+nmu1) ... 140s Setting up gcc-13-aarch64-linux-gnu (13.2.0-19ubuntu1) ... 140s Setting up gcc-13 (13.2.0-19ubuntu1) ... 140s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1ubuntu1) ... 140s Setting up cpp (4:13.2.0-7ubuntu1) ... 140s Setting up g++-13-aarch64-linux-gnu (13.2.0-19ubuntu1) ... 140s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 140s Setting up g++-13 (13.2.0-19ubuntu1) ... 140s Setting up libtool (2.4.7-7) ... 140s Setting up libhts-dev:arm64 (1.19+ds-1.1build2) ... 140s Setting up gcc (4:13.2.0-7ubuntu1) ... 140s Setting up dh-autoreconf (20) ... 140s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 140s Setting up debhelper (13.14.1ubuntu5) ... 140s Setting up g++ (4:13.2.0-7ubuntu1) ... 140s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 140s Setting up build-essential (12.10ubuntu1) ... 140s Setting up autopkgtest-satdep (0) ... 140s Processing triggers for man-db (2.12.0-3) ... 141s Processing triggers for install-info (7.1-3) ... 141s Processing triggers for libc-bin (2.39-0ubuntu6) ... 147s (Reading database ... 79608 files and directories currently installed.) 147s Removing autopkgtest-satdep (0) ... 148s autopkgtest [17:14:06]: test run-unit-test: [----------------------- 148s + pkg=htslib 148s + '[' /tmp/autopkgtest.T4wPj3/autopkgtest_tmp = '' ']' 148s + cp -aL /usr/share/htslib-test/Makefile /usr/share/htslib-test/annot-tsv.c /usr/share/htslib-test/bcf_sr_sort.c /usr/share/htslib-test/bcf_sr_sort.h /usr/share/htslib-test/bgzf.c /usr/share/htslib-test/bgzip.c /usr/share/htslib-test/config.h /usr/share/htslib-test/config.mk /usr/share/htslib-test/config_vars.h /usr/share/htslib-test/cram /usr/share/htslib-test/errmod.c /usr/share/htslib-test/faidx.c /usr/share/htslib-test/fuzz_settings.h /usr/share/htslib-test/header.c /usr/share/htslib-test/header.h /usr/share/htslib-test/hfile.c /usr/share/htslib-test/hfile_gcs.c /usr/share/htslib-test/hfile_internal.h /usr/share/htslib-test/hfile_libcurl.c /usr/share/htslib-test/hfile_s3.c /usr/share/htslib-test/hfile_s3_write.c /usr/share/htslib-test/hts.c /usr/share/htslib-test/hts_expr.c /usr/share/htslib-test/hts_internal.h /usr/share/htslib-test/hts_os.c /usr/share/htslib-test/hts_time_funcs.h /usr/share/htslib-test/htscodecs.mk /usr/share/htslib-test/htscodecs_bundled.mk /usr/share/htslib-test/htscodecs_external.mk /usr/share/htslib-test/htsfile.c /usr/share/htslib-test/htslib.mk /usr/share/htslib-test/htslib_static.mk /usr/share/htslib-test/htslib_vars.mk /usr/share/htslib-test/kfunc.c /usr/share/htslib-test/kstring.c /usr/share/htslib-test/md5.c /usr/share/htslib-test/multipart.c /usr/share/htslib-test/os /usr/share/htslib-test/plugin.c /usr/share/htslib-test/probaln.c /usr/share/htslib-test/realn.c /usr/share/htslib-test/regidx.c /usr/share/htslib-test/region.c /usr/share/htslib-test/sam.c /usr/share/htslib-test/sam_internal.h /usr/share/htslib-test/sam_mods.c /usr/share/htslib-test/synced_bcf_reader.c /usr/share/htslib-test/tabix.c /usr/share/htslib-test/tbx.c /usr/share/htslib-test/test /usr/share/htslib-test/textutils.c /usr/share/htslib-test/textutils_internal.h /usr/share/htslib-test/thread_pool.c /usr/share/htslib-test/thread_pool_internal.h /usr/share/htslib-test/vcf.c /usr/share/htslib-test/vcf_sweep.c /usr/share/htslib-test/vcfutils.c /usr/share/htslib-test/version.h /usr/share/htslib-test/version.sh /tmp/autopkgtest.T4wPj3/autopkgtest_tmp 148s + cp -aL htslib.pc.in /tmp/autopkgtest.T4wPj3/autopkgtest_tmp 148s + cp -aL htslib.map /tmp/autopkgtest.T4wPj3/autopkgtest_tmp 148s + cd /tmp/autopkgtest.T4wPj3/autopkgtest_tmp 148s + sed -i 's#\$(HTSPREFIX)#/usr/include/#g' htslib_vars.mk 148s + sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk 148s + CFLAGS='-O2 -fno-strict-aliasing -fno-code-hoisting' 148s + grep sse /proc/cpuinfo 148s + export CFLAGS 148s + make -e check 149s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o kfunc.o kfunc.c 149s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o kstring.o kstring.c 149s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bcf_sr_sort.o bcf_sr_sort.c 151s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bgzf.o bgzf.c 152s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o errmod.o errmod.c 152s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o faidx.o faidx.c 153s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o header.o header.c 155s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hfile.o hfile.c 155s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts.o hts.c 159s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts_expr.o hts_expr.c 159s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts_os.o hts_os.c 160s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o md5.o md5.c 160s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o multipart.o multipart.c 160s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o probaln.o probaln.c 161s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o realn.o realn.c 161s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o regidx.o regidx.c 162s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o region.o region.c 162s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam.o sam.c 168s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam_mods.o sam_mods.c 168s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o synced_bcf_reader.o synced_bcf_reader.c 169s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcf_sweep.o vcf_sweep.c 170s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tbx.o tbx.c 170s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o textutils.o textutils.c 171s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o thread_pool.o thread_pool.c 171s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcf.o vcf.c 179s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcfutils.o vcfutils.c 180s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_codecs.o cram/cram_codecs.c 182s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_decode.o cram/cram_decode.c 184s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_encode.o cram/cram_encode.c 186s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_external.o cram/cram_external.c 186s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_index.o cram/cram_index.c 186s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_io.o cram/cram_io.c 189s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_stats.o cram/cram_stats.c 189s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/mFILE.o cram/mFILE.c 189s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/open_trace_file.o cram/open_trace_file.c 189s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/pooled_alloc.o cram/pooled_alloc.c 189s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/string_alloc.o cram/string_alloc.c 189s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -c -o plugin.o plugin.c 190s ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o plugin.o 190s ranlib libhts.a 190s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o kfunc.pico kfunc.c 190s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o kstring.pico kstring.c 190s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c 191s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o bgzf.pico bgzf.c 192s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o errmod.pico errmod.c 192s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o faidx.pico faidx.c 193s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o header.pico header.c 196s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile.pico hfile.c 196s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts.pico hts.c 199s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts_expr.pico hts_expr.c 199s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts_os.pico hts_os.c 200s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o md5.pico md5.c 200s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o multipart.pico multipart.c 200s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o probaln.pico probaln.c 200s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o realn.pico realn.c 200s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o regidx.pico regidx.c 201s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o region.pico region.c 201s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o sam.pico sam.c 205s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o sam_mods.pico sam_mods.c 205s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c 206s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcf_sweep.pico vcf_sweep.c 206s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o tbx.pico tbx.c 206s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o textutils.pico textutils.c 207s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o thread_pool.pico thread_pool.c 207s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcf.pico vcf.c 212s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcfutils.pico vcfutils.c 213s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c 214s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c 216s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c 219s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_external.pico cram/cram_external.c 219s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_index.pico cram/cram_index.c 220s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_io.pico cram/cram_io.c 222s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c 222s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/mFILE.pico cram/mFILE.c 222s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c 222s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c 222s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c 223s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -fPIC -c -o plugin.pico plugin.c 223s gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico plugin.pico -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 223s ln -sf libhts.so libhts.so.3 223s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o annot-tsv.o annot-tsv.c 224s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 224s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bgzip.o bgzip.c 224s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread 224s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o htsfile.o htsfile.c 224s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread 224s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tabix.o tabix.c 225s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread 225s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c 225s gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcurl -lpthread 225s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_gcs.pico hfile_gcs.c 225s gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 226s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_s3.pico hfile_s3.c 226s gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lpthread 226s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c 227s gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread 227s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/hts_endian.o test/hts_endian.c 227s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm 227s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/fieldarith.o test/fieldarith.c 227s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 227s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/hfile.o test/hfile.c 228s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 228s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/pileup.o test/pileup.c 228s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 228s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/pileup_mod.o test/pileup_mod.c 228s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 228s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/plugins-dlhts.o test/plugins-dlhts.c 228s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm 228s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/sam.o test/sam.c 230s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 230s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_bgzf.o test/test_bgzf.c 231s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 231s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_expr.o test/test_expr.c 231s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 231s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_faidx.o test/test_faidx.c 231s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 231s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_kfunc.o test/test_kfunc.c 231s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 231s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_kstring.o test/test_kstring.c 231s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 231s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_mod.o test/test_mod.c 232s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 232s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_realn.o test/test_realn.c 232s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 232s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-regidx.o test/test-regidx.c 232s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 232s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_str2int.o test/test_str2int.c 232s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 232s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_time_funcs.o test/test_time_funcs.c 232s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o 232s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_view.o test/test_view.c 233s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 233s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_index.o test/test_index.c 233s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 233s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-vcf-api.o test/test-vcf-api.c 233s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 233s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c 233s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 233s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf-sr.o test/test-bcf-sr.c 233s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 234s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c 234s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf-translate.o test/test-bcf-translate.c 234s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 234s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-parse-reg.o test/test-parse-reg.c 234s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 234s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_introspection.o test/test_introspection.c 234s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 234s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c 239s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 239s sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp 239s sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk 239s sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc 239s test/hts_endian 239s test/test_expr 239s test/test_kfunc 239s test/test_kstring 239s test/test_str2int 239s test/test_time_funcs 239s test/fieldarith test/fieldarith.sam 239s test/hfile 240s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 240s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ 240s fi 240s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 240s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ 240s fi 240s test/test_bgzf test/bgziptest.txt 240s test/test-parse-reg -t test/colons.bam 241s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead 241s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead 241s Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" 241s Expected error: [E::hts_parse_region] Unexpected string "x" after region 241s Expected error: [E::hts_parse_region] Unexpected string "y" after region 241s Expected error: [E::hts_parse_region] Unexpected string "chr3" after region 241s cd test/faidx && ./test-faidx.sh faidx.tst 241s Testing faidx... 241s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai 241s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 241s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo 241s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent 241s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 241s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 241s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 241s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai 241s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 241s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 241s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 241s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent 241s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 241s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 241s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 241s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 241s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 241s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 241s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 241s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 241s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 241s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 241s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 241s PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai 241s PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225 241s 241s Expected passes: 25 241s Unexpected passes: 0 241s Expected failures: 0 241s Unexpected failures: 0 241s cd test/sam_filter && ./filter.sh filter.tst 241s Testing sam_filter... 241s PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam 241s PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam 241s PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam 241s PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam 241s PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam 241s PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam 241s PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam 241s PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' 241s PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' 241s PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' 241s PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' 241s PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' 241s PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' 241s PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' 241s PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' 241s PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' 241s PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' 241s PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' 241s 241s Expected passes: 18 241s Unexpected passes: 0 241s Expected failures: 0 241s Unexpected failures: 0 241s cd test/tabix && ./test-tabix.sh tabix.tst 241s Testing tabix... 241s PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz 241s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 241s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 241s PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz 241s PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 241s PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 241s PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) 241s PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz 241s PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 241s PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz 241s PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 241s PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz 241s PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 241s PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 241s 241s Expected passes: 14 241s Unexpected passes: 0 241s Expected failures: 0 241s Unexpected failures: 0 241s cd test/mpileup && ./test-pileup.sh mpileup.tst 241s Testing (m)pileup... 241s PASS : $pileup mp_D.sam 241s PASS : $pileup -m mp_D.sam 241s PASS : $pileup mp_DI.sam 241s PASS : $pileup -m mp_DI.sam 241s PASS : $pileup mp_I.sam 241s PASS : $pileup -m mp_I.sam 241s PASS : $pileup mp_P.sam 241s PASS : $pileup -m mp_P.sam 241s PASS : $pileup mp_ID.sam 241s PASS : $pileup -m mp_ID.sam 241s PASS : $pileup mp_N.sam 241s PASS : $pileup -m mp_N.sam 241s PASS : $pileup mp_N2.sam 241s PASS : $pileup -m mp_N2.sam 241s PASS : $pileup c1#pad1.sam 241s PASS : $pileup -m c1#pad1.sam 241s PASS : $pileup c1#pad2.sam 242s PASS : $pileup -m c1#pad2.sam 242s PASS : $pileup c1#pad3.sam 242s PASS : $pileup -m c1#pad3.sam 242s PASS : $pileup -m small.bam 242s 242s Expected passes: 21 242s Unexpected passes: 0 242s Expected failures: 0 242s Unexpected failures: 0 242s cd test/fastq && ./test-fastq.sh 242s Testing fastq support 242s PASS : $tview minimal.fq 242s PASS : $tview minimal.fa 242s PASS : $tview multiline.fq 242s PASS : $tview multiline.fa 242s PASS : $tview -i fastq_aux longline.fq 242s PASS : $tview single.fq 242s PASS : $tview single.fa 242s PASS : $tview -i fastq_aux single.fq 242s PASS : $tview -i fastq_aux single.fa 242s PASS : $tview interleaved.fq 242s PASS : $tview interleaved.fa 242s PASS : $tview -i fastq_aux interleaved.fq 242s PASS : $tview -i fastq_aux interleaved.fa 242s PASS : $tview -i fastq_casava interleaved_casava.fq 242s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq 242s PASS : $tview -i fastq_casava interleaved_casava.fa 242s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa 242s PASS : $tview -i fastq_casava filter_casava.fq 242s PASS : $tview -i fastq_casava filter_casava.fa 242s PASS : $tview -i fastq_aux r1.fq 242s PASS : $tview -i fastq_aux r2.fq 242s PASS : $tview -i fastq_aux r1.fa 242s PASS : $tview -i fastq_aux r2.fa 242s PASS : $tview -i fastq_name2 name2.fq 242s PASS : $tview -i fastq_name2 name2.fa 242s PASS : $tview -f minimal.sam 242s PASS : $tview -F minimal.sam 242s PASS : $tview -f -o fastq_aux single_aux.sam 242s PASS : $tview -F -o fastq_aux single_aux.sam 242s PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam 242s PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam 242s PASS : $tview -f -o fastq_casava inter_casava.sam 242s PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 242s PASS : $tview -F -o fastq_casava inter_casava.sam 242s PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 242s PASS : $tview -f -o fastq_casava filter_casava.sam 242s PASS : $tview -F -o fastq_casava filter_casava.sam 242s PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam 242s PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam 242s PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam 242s PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam 242s 242s Expected passes: 41 242s Unexpected passes: 0 242s Expected failures: 0 242s Unexpected failures: 0 242s cd test/base_mods && ./base-mods.sh base-mods.tst 242s Testing base-modifications... 242s PASS : $test_mod MM-chebi.sam 242s PASS : $test_mod MM-double.sam 242s PASS : $test_mod MM-multi.sam 242s PASS : $test_mod MM-explicit.sam 242s PASS : $test_mod -x MM-explicit.sam 242s PASS : $test_mod -f 1 MM-explicit.sam 242s PASS : $test_mod MM-not-all-modded.sam 242s PASS : $pileup_mod < MM-pileup.sam 242s PASS : $pileup_mod < MM-pileup2.sam 242s PASS : $pileup_mod < MM-MNp.sam 242s PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) 242s PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) 242s 242s Expected passes: 12 242s Unexpected passes: 0 242s Expected failures: 0 242s Unexpected failures: 0 242s REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq 242s (Expect trailing 'x' message for " -1,001x") 242s [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] 242s (Expect trailing 'k' message for "1.5e+3k") 242s [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] 242s (Expect dropped fraction message for "12.3456k") 242s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 242s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 242s (Expect invalid numeric message for "A") 242s [W::hts_parse_decimal] Invalid numeric value A[truncated] 242s (Expect invalid numeric message for "G") 242s [W::hts_parse_decimal] Invalid numeric value G[truncated] 242s (Expect invalid numeric message for " +/-") 242s [W::hts_parse_decimal] Invalid numeric value +/-[truncated] 242s (Expect invalid numeric message for " -.e+9999") 242s [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] 242s test/test-regidx 242s cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} 243s bgzip round-trip no threads: .. ok 243s 243s bgzip text mode round-trip no threads: .. ok 243s 243s bgzip -b no threads: .. ok 243s 243s bgzip -b -I no threads: .. ok 243s 243s bgzip multifile no threads: .. ok 243s 243s bgzip round-trip 4 threads: .. ok 243s 243s bgzip text mode round-trip 4 threads: .. ok 243s 243s bgzip -b 4 threads: .. ok 243s 243s bgzip -b -I 4 threads: .. ok 243s 244s bgzip multifile 4 threads: .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/GNNswgrs3l/index.bam.csi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.sam > /tmp/GNNswgrs3l/index.bam 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -c /tmp/GNNswgrs3l/index.bam 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -l 0 -b -m 0 -x /tmp/GNNswgrs3l/index.bam.bai /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.sam > /tmp/GNNswgrs3l/index.bam 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -b /tmp/GNNswgrs3l/index.bam 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/GNNswgrs3l/index.sam.gz.csi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.sam > /tmp/GNNswgrs3l/index.sam.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -c /tmp/GNNswgrs3l/index.sam.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/GNNswgrs3l/index.sam.gz.bai /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.sam > /tmp/GNNswgrs3l/index.sam.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -b /tmp/GNNswgrs3l/index.sam.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/GNNswgrs3l/index.sam.gz.csi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index_dos.sam > /tmp/GNNswgrs3l/index.sam.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -c /tmp/GNNswgrs3l/index.sam.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/GNNswgrs3l/index.sam.gz.bai /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index_dos.sam > /tmp/GNNswgrs3l/index.sam.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -b /tmp/GNNswgrs3l/index.sam.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -l 0 -C -x /tmp/GNNswgrs3l/index.cram.crai /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.sam > /tmp/GNNswgrs3l/index.cram 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index /tmp/GNNswgrs3l/index.cram 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/GNNswgrs3l/index.bcf.csi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.vcf > /tmp/GNNswgrs3l/index.bcf 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -c /tmp/GNNswgrs3l/index.bcf 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/GNNswgrs3l/index.vcf.gz.csi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.vcf > /tmp/GNNswgrs3l/index.vcf.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -c /tmp/GNNswgrs3l/index.vcf.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/GNNswgrs3l/index.vcf.gz.tbi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.vcf > /tmp/GNNswgrs3l/index.vcf.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -t /tmp/GNNswgrs3l/index.vcf.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/tabix /tmp/GNNswgrs3l/index.vcf.gz##idx##/tmp/GNNswgrs3l/index.vcf.gz.tbi 1:10000060-10000060 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view /tmp/GNNswgrs3l/index2.bam 1:1000000-1000000 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view /tmp/GNNswgrs3l/index2.bam 1:2000000-2000000 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view /tmp/GNNswgrs3l/index2.bam 2:1000000-1000000 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view /tmp/GNNswgrs3l/index2.bam 2:2000000-2000000 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/GNNswgrs3l/index.bam.csi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.sam > /tmp/GNNswgrs3l/index.bam 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -c /tmp/GNNswgrs3l/index.bam 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 0 -x /tmp/GNNswgrs3l/index.bam.bai /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.sam > /tmp/GNNswgrs3l/index.bam 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -b /tmp/GNNswgrs3l/index.bam 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/GNNswgrs3l/index.sam.gz.csi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.sam > /tmp/GNNswgrs3l/index.sam.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -c /tmp/GNNswgrs3l/index.sam.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/GNNswgrs3l/index.sam.gz.bai /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.sam > /tmp/GNNswgrs3l/index.sam.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -b /tmp/GNNswgrs3l/index.sam.gz 244s .. ok 244s 244s test_index: 244s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/GNNswgrs3l/index.sam.gz.csi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index_dos.sam > /tmp/GNNswgrs3l/index.sam.gz 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -c /tmp/GNNswgrs3l/index.sam.gz 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/GNNswgrs3l/index.sam.gz.bai /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index_dos.sam > /tmp/GNNswgrs3l/index.sam.gz 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -b /tmp/GNNswgrs3l/index.sam.gz 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -@4 -l 0 -C -x /tmp/GNNswgrs3l/index.cram.crai /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.sam > /tmp/GNNswgrs3l/index.cram 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index /tmp/GNNswgrs3l/index.cram 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/GNNswgrs3l/index.bcf.csi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.vcf > /tmp/GNNswgrs3l/index.bcf 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -c /tmp/GNNswgrs3l/index.bcf 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/GNNswgrs3l/index.vcf.gz.csi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.vcf > /tmp/GNNswgrs3l/index.vcf.gz 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -c /tmp/GNNswgrs3l/index.vcf.gz 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/GNNswgrs3l/index.vcf.gz.tbi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/index.vcf > /tmp/GNNswgrs3l/index.vcf.gz 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -t /tmp/GNNswgrs3l/index.vcf.gz 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/tabix /tmp/GNNswgrs3l/index.vcf.gz##idx##/tmp/GNNswgrs3l/index.vcf.gz.tbi 1:10000060-10000060 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view /tmp/GNNswgrs3l/index2.bam 1:1000000-1000000 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view /tmp/GNNswgrs3l/index2.bam 1:2000000-2000000 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view /tmp/GNNswgrs3l/index2.bam 2:1000000-1000000 245s .. ok 245s 245s test_index: 245s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view /tmp/GNNswgrs3l/index2.bam 2:2000000-2000000 245s .. ok 245s 245s test_view testing multi-ref CRAM modes: 245s ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 245s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 245s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 245s ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 245s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 245s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 245s ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 245s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 245s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 246s .. ok 246s 246s test_view testing multi-ref CRAM modes: 246s ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 246s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 246s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 246s ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 246s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 246s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 246s ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 246s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 246s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 246s .. ok 246s 246s test_view testing auxf#values.sam, ref auxf.fa: 246s ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 246s ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 246s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 246s ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 246s ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 246s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 246s ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 246s ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 246s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 246s ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 246s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 246s .. ok 246s 246s test_view testing c1#bounds.sam, ref c1.fa: 246s ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 246s ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 246s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 246s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 246s ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 246s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 246s ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 246s ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 246s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 246s .. ok 246s 246s test_view testing c1#clip.sam, ref c1.fa: 246s ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 246s ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 246s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 246s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 246s ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 246s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 246s ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 246s ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 246s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 246s .. ok 246s 246s test_view testing c1#noseq.sam, ref c1.fa: 246s ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 246s ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 246s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 246s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 246s ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 246s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 247s ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 247s ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 247s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 247s .. ok 247s 247s test_view testing c1#pad1.sam, ref c1.fa: 247s ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 247s ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 247s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 247s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 247s ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 247s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 247s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 247s ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 247s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 247s .. ok 247s 247s test_view testing c1#pad2.sam, ref c1.fa: 247s ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 247s ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 247s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 247s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 247s ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 247s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 247s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 247s ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 247s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 247s .. ok 247s 247s test_view testing c1#pad3.sam, ref c1.fa: 247s ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 247s ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 247s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 247s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 247s ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 247s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 247s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 247s ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 247s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 247s .. ok 247s 247s test_view testing c1#unknown.sam, ref c1.fa: 247s ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 247s ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 247s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 247s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 247s ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 247s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 247s ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 247s ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 247s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 247s .. ok 247s 247s test_view testing c2#pad.sam, ref c2.fa: 247s ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 247s ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 247s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 247s ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 247s ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 247s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 247s ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 247s ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 247s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 247s .. ok 247s 247s test_view testing ce#1.sam, ref ce.fa: 247s ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam 247s ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ 248s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 248s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 248s ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 248s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 248s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 248s ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 248s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 248s .. ok 248s 248s test_view testing ce#1000.sam, ref ce.fa: 248s ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam 248s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 248s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 248s ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 248s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 248s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 248s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 249s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 249s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 249s ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 249s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 249s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 249s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 249s ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 251s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 251s .. ok 251s 251s test_view testing ce#2.sam, ref ce.fa: 251s ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam 251s ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ 251s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 251s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 251s ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 251s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 252s ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 252s ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 252s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 252s .. ok 252s 252s test_view testing ce#5.sam, ref ce.fa: 252s ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam 252s ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ 252s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 252s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 252s ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 252s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 252s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 252s ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 252s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 252s .. ok 252s 252s test_view testing ce#5b.sam, ref ce.fa: 252s ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 252s ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 252s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 252s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 252s ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 252s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 252s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 252s ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 252s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 252s ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 252s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 252s .. ok 252s 252s test_view testing ce#large_seq.sam, ref ce.fa: 252s ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 252s ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 252s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 252s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 252s ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 252s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 252s ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 252s ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 252s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 252s .. ok 252s 252s test_view testing ce#supp.sam, ref ce.fa: 252s ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 252s ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 252s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 252s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 252s ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 252s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 252s ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 252s ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 252s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 252s .. ok 252s 252s test_view testing ce#tag_depadded.sam, ref ce.fa: 252s ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 253s ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 253s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 253s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 253s ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 253s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 253s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 253s ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 253s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 253s .. ok 253s 253s test_view testing ce#tag_padded.sam, ref ce.fa: 253s ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 253s ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 253s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 253s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 253s ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 253s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 253s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 253s ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 253s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 253s .. ok 253s 253s test_view testing ce#unmap.sam, ref ce.fa: 253s ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 253s ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 253s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 253s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 253s ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 253s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 253s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 253s ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 253s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 253s .. ok 253s 253s test_view testing ce#unmap1.sam, ref ce.fa: 253s ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 253s ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 253s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 253s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 253s ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 253s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 253s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 253s ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 253s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 253s .. ok 253s 253s test_view testing ce#unmap2.sam, ref ce.fa: 253s ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 253s ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 253s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 253s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 253s ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 253s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 253s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 253s ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 253s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 253s .. ok 253s 253s test_view testing md#1.sam, ref md.fa: 253s ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam 253s ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ 253s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 253s ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 253s ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ 253s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 253s ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 253s ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 253s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 253s .. ok 253s 253s test_view testing xx#blank.sam, ref xx.fa: 253s ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 253s ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 253s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 253s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 253s ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 253s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 253s ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 253s ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 253s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 253s .. ok 253s 253s test_view testing xx#large_aux.sam, ref xx.fa: 253s ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 253s ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 253s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 253s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 253s ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 253s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 253s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 253s ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 253s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 253s ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 253s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 253s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 253s .. ok 253s 253s test_view testing xx#large_aux2.sam, ref xx.fa: 253s ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 253s ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 253s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 253s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 253s ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 253s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 253s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 253s ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 254s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 254s .. ok 254s 254s test_view testing xx#MD.sam, ref xx.fa: 254s ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 254s ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 254s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 254s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 254s ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 254s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 254s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 254s ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 254s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 254s .. ok 254s 254s test_view testing xx#MD2.sam, ref xx.fa: 254s ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 254s ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 254s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 254s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 254s ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 254s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 254s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 254s ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 254s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 254s .. ok 254s 254s test_view testing xx#minimal.sam, ref xx.fa: 254s ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 254s ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 254s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 254s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 254s ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 254s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 254s ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 254s ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 254s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 254s .. ok 254s 254s test_view testing xx#pair.sam, ref xx.fa: 254s ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 254s ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 254s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 254s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 254s ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 254s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 254s ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 254s ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 254s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 254s .. ok 254s 254s test_view testing xx#repeated.sam, ref xx.fa: 254s ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 254s ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 254s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 254s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 254s ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 254s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 254s ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 254s ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 254s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 254s .. ok 254s 254s test_view testing xx#rg.sam, ref xx.fa: 254s ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 254s ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 254s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 254s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 254s ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 254s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 254s ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 254s ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 254s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 254s .. ok 254s 254s test_view testing xx#tlen.sam, ref xx.fa: 254s ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 254s ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 254s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 254s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 254s ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 254s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 254s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 254s ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 254s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 254s .. ok 254s 254s test_view testing xx#tlen2.sam, ref xx.fa: 254s ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 254s ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 254s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 255s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 255s ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 255s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 255s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 255s ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 255s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 255s .. ok 255s 255s test_view testing xx#triplet.sam, ref xx.fa: 255s ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 255s ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 255s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 255s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 255s ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 255s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 255s ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 255s ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 255s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 255s .. ok 255s 255s test_view testing xx#unsorted.sam, ref xx.fa: 255s ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 255s ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 255s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 255s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 255s ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 255s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 255s ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 255s ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 255s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 255s .. ok 255s 255s test_view testing embed_ref=2: 255s ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam 255s [W::cram_get_ref] Failed to populate reference for id 0 255s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 255s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 255s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 255s ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 255s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 255s .. ok 255s 255s test_view testing region queries: 255s ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 255s ./compare_sam.pl range.tmp range.out 255s ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 255s ./compare_sam.pl range.tmp range.out 255s .. ok 255s 255s test_view testing BAM files with absent @SQ lines: 255s ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 255s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 255s ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 255s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 255s .. ok 255s 255s test_view testing large (> 2Gbases) positions: 255s ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 255s ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 255s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 255s test_view: 255s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 255s .. ok 255s 255s ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 255s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 255s ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 255s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 255s .. ok 255s 255s test_view testing auxf#values.sam, ref auxf.fa: 255s ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 255s ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 255s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 255s ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 255s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 255s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 255s ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 255s ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 255s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 255s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram 255s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 255s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 255s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram 255s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 255s This is a technology demonstration that should not be used for archival data. 256s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 256s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 256s ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 256s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 256s .. ok 256s 256s test_view testing c1#bounds.sam, ref c1.fa: 256s ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 256s ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 256s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 256s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 256s ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 256s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 256s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 256s ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 256s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 256s .. ok 256s 256s test_view testing c1#clip.sam, ref c1.fa: 256s ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 256s ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 256s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 256s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 256s ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 256s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 256s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 256s ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 256s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 256s .. ok 256s 256s test_view testing c1#noseq.sam, ref c1.fa: 256s ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 256s ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 256s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 256s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 256s ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 256s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 256s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 256s ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 256s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 256s .. ok 256s 256s test_view testing c1#pad1.sam, ref c1.fa: 256s ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 256s ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 256s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 256s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 256s ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 256s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 256s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 256s ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 256s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 257s .. ok 257s 257s test_view testing c1#pad2.sam, ref c1.fa: 257s ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 257s ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 257s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 257s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 257s ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 257s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 257s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 257s ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 257s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 257s .. ok 257s 257s test_view testing c1#pad3.sam, ref c1.fa: 257s ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 257s ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 257s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 257s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 257s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 257s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 257s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 257s ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 257s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 257s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram 257s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 257s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 257s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram 257s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 257s This is a technology demonstration that should not be used for archival data. 257s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 257s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 257s .. ok 257s 257s test_view testing c1#unknown.sam, ref c1.fa: 257s ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 257s ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 257s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 257s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 257s ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 257s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 257s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 257s ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 257s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 257s .. ok 257s 257s test_view testing c2#pad.sam, ref c2.fa: 257s ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 257s ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 257s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 257s ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 257s ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 257s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 257s ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 258s ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 258s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 258s .. ok 258s 258s test_view testing ce#1.sam, ref ce.fa: 258s ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam 258s ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ 258s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 258s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 258s ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 258s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 258s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 258s ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 258s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 258s .. ok 258s 258s test_view testing ce#1000.sam, ref ce.fa: 258s ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam 258s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 258s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 258s ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 258s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 258s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 258s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 258s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 258s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 258s ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 258s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 258s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 258s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 258s ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 258s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 258s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms 258s ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ 258s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ 258s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram 258s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 258s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 258s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram 258s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 259s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 259s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram 259s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 259s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 259s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram 259s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 260s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 260s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram 260s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 260s This is a technology demonstration that should not be used for archival data. 260s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 260s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 260s .. ok 260s 260s test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: 260s ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam 261s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ 261s ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ 261s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram 261s ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ 261s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ 262s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram 262s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 262s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 262s .. ok 262s 262s test_view testing ce#2.sam, ref ce.fa: 262s ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam 262s ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ 263s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 263s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 263s ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 263s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 263s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 264s ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 264s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 264s .. ok 264s 264s test_view testing ce#5.sam, ref ce.fa: 264s ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam 264s ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ 264s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 264s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 264s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 264s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 264s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 264s ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 264s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 264s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms 264s ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ 264s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ 264s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram 264s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 264s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 264s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram 264s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 264s This is a technology demonstration that should not be used for archival data. 264s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 265s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 265s .. ok 265s 265s test_view testing ce#5b.sam, ref ce.fa: 265s ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 265s ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 265s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 265s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 265s ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 265s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 265s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 265s ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 265s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 265s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms 265s ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ 265s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ 265s ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 265s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 265s .. ok 265s 265s test_view testing ce#large_seq.sam, ref ce.fa: 265s ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 265s ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 265s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 265s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 265s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 265s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 265s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 265s ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 266s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 266s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 266s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 266s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 266s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram 266s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 266s This is a technology demonstration that should not be used for archival data. 266s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 266s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 266s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram 266s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 266s This is a technology demonstration that should not be used for archival data. 267s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 267s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 267s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram 267s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 267s This is a technology demonstration that should not be used for archival data. 267s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 267s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 267s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 267s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 267s This is a technology demonstration that should not be used for archival data. 267s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 267s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 267s .. ok 267s 267s test_view testing ce#supp.sam, ref ce.fa: 267s ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 268s ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 268s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 268s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 268s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 268s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 268s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 268s ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 268s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 268s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram 268s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 268s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 268s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram 268s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 268s This is a technology demonstration that should not be used for archival data. 268s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 269s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 269s .. ok 269s 269s test_view testing ce#tag_depadded.sam, ref ce.fa: 269s ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 269s ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 269s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 269s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 269s ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 269s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 269s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 269s ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 269s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 269s .. ok 269s 269s test_view testing ce#tag_padded.sam, ref ce.fa: 269s ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 269s ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 269s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 269s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 269s ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 269s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 270s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 270s ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 270s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 270s .. ok 270s 270s test_view testing ce#unmap.sam, ref ce.fa: 270s ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 270s ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 270s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 270s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 270s ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 270s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 270s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 270s ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 270s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 270s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms 270s ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ 270s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ 270s .. ok 270s 270s test_view testing ce#unmap1.sam, ref ce.fa: 270s ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 270s ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 270s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 270s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 270s ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 270s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 270s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 270s ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 270s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 270s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms 270s ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ 270s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ 270s .. ok 270s 270s test_view testing ce#unmap2.sam, ref ce.fa: 270s ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 270s ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 270s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 270s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 270s ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 270s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 270s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 270s ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 270s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 270s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms 270s ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ 270s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ 270s .. ok 270s 270s test_view testing md#1.sam, ref md.fa: 270s ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam 270s ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ 270s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 270s ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 270s ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ 270s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 270s ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 270s ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 270s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 270s .. ok 270s 270s test_view testing xx#blank.sam, ref xx.fa: 270s ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 270s ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 270s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 270s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 271s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 271s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 271s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 271s ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 271s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 271s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms 271s ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ 271s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ 271s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram 271s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 271s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 271s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram 271s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 271s This is a technology demonstration that should not be used for archival data. 271s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 271s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 271s .. ok 271s 271s test_view testing xx#large_aux.sam, ref xx.fa: 271s ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 271s ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 271s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 271s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 271s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 271s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 271s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 271s ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 271s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 271s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 271s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 271s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 271s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram 271s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 271s This is a technology demonstration that should not be used for archival data. 271s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 271s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 271s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram 271s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 271s This is a technology demonstration that should not be used for archival data. 271s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 271s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 271s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram 271s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 271s This is a technology demonstration that should not be used for archival data. 272s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 272s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 272s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 272s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 272s This is a technology demonstration that should not be used for archival data. 272s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 272s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 272s ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 272s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 272s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 272s .. ok 272s 272s test_view testing xx#large_aux2.sam, ref xx.fa: 272s ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 272s ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 272s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 272s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 272s ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 272s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 272s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 272s ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 272s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 272s .. ok 272s 272s test_view testing xx#MD.sam, ref xx.fa: 272s ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 272s ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 272s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 272s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 272s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 272s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 272s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 272s ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 272s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 272s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram 272s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 272s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 272s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram 272s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 272s This is a technology demonstration that should not be used for archival data. 272s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 273s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 273s .. ok 273s 273s test_view testing xx#MD2.sam, ref xx.fa: 273s ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 273s ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 273s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 273s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 273s ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 273s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 273s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 273s ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 273s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 273s .. ok 273s 273s test_view testing xx#minimal.sam, ref xx.fa: 273s ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 273s ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 273s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 273s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 273s ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 273s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 273s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 273s ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 273s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 273s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms 273s ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ 273s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ 273s .. ok 273s 273s test_view testing xx#pair.sam, ref xx.fa: 273s ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 273s ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 273s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 273s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 273s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 273s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 273s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 273s ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 273s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 273s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram 273s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 273s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 273s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram 273s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 273s This is a technology demonstration that should not be used for archival data. 273s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 273s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 273s .. ok 273s 273s test_view testing xx#repeated.sam, ref xx.fa: 273s ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 273s ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 274s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 274s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 274s ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 274s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 274s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 274s ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 274s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 274s .. ok 274s 274s test_view testing xx#rg.sam, ref xx.fa: 274s ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 274s ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 274s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 274s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 274s ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 274s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 274s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 274s ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 274s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 274s .. ok 274s 274s test_view testing xx#tlen.sam, ref xx.fa: 274s ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 274s ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 274s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 274s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 274s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 274s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 274s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 274s ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 274s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 274s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms 274s ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ 274s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ 274s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram 274s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 274s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 274s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram 274s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 274s This is a technology demonstration that should not be used for archival data. 274s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 274s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 274s .. ok 274s 274s test_view testing xx#tlen2.sam, ref xx.fa: 274s ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 274s ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 274s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 275s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 275s ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 275s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 275s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 275s ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 275s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 275s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms 275s ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ 275s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ 275s .. ok 275s 275s test_view testing xx#triplet.sam, ref xx.fa: 275s ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 275s ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 275s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 275s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 275s ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 275s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 275s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 275s ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 275s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 275s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms 275s ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ 275s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ 275s .. ok 275s 275s test_view testing xx#unsorted.sam, ref xx.fa: 275s ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 275s ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 275s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 275s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 275s ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 275s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 275s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 275s ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 275s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 275s .. ok 275s 275s test_view testing embed_ref=2: 275s ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam 275s [W::cram_get_ref] Failed to populate reference for id 0 275s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 275s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 275s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 275s ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 275s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 275s .. ok 275s 275s test_view testing region queries: 275s ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 275s ./compare_sam.pl range.tmp range.out 275s ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 275s ./compare_sam.pl range.tmp range.out 275s .. ok 275s 275s test_view testing BAM files with absent @SQ lines: 275s ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 275s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 275s ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 275s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 275s .. ok 275s 275s test_view testing large (> 2Gbases) positions: 275s ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 275s ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 275s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 275s test_view: 275s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 276s .. ok 276s 276s ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 276s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 276s ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 276s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 276s .. ok 276s 276s 276s test_MD testing xx#MD.sam, ref xx.fa: 276s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 276s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 276s ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ 276s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 276s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 276s ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ 276s Checking for MD/NM in xx#MD.sam 276s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 276s ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 276s ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ 276s .. ok 276s 276s 276s test_MD testing xx#MD2.sam, ref xx.fa: 276s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 276s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 276s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ 276s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 276s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 276s ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ 276s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 276s ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 276s ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ 276s .. ok 276s 276s test_vcf_api: 276s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-vcf-api /tmp/GNNswgrs3l/test-vcf-api.bcf 276s .. ok 276s 276s test_bcf2vcf: 276s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/tabix/vcf_file.bcf 276s .. ok 276s 276s test_vcf_sweep: 276s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-vcf-sweep /tmp/GNNswgrs3l/test-vcf-api.bcf 276s .. ok 276s 276s test_vcf_various: 276s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/htsfile -ch /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-vcf-hdr-in.vcf 276s .. ok 276s 276s test_vcf_various: 276s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/formatcols.vcf 276s .. ok 276s 276s test_vcf_various: 276s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/noroundtrip.vcf 276s .. ok 276s 276s test_vcf_various: 276s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/formatmissing.vcf 276s .. ok 276s 276s test_vcf_various: 276s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/vcf_meta_meta.vcf 276s .. ok 276s 276s test_vcf_various: 276s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/modhdr.vcf.gz chr22:1-2 276s .. ok 276s 276s test-bcf-sr: 276s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/GNNswgrs3l -s 74452500 276s .. ok 276s 276s test-bcf-sr: 276s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/GNNswgrs3l -s 34270147 277s .. ok 277s 277s test-bcf-sr: 277s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/GNNswgrs3l -s 11108528 277s .. ok 277s 277s test-bcf-sr: 277s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/GNNswgrs3l -s 42233895 277s .. ok 277s 277s test-bcf-sr: 277s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/GNNswgrs3l -s 8111117 278s .. ok 278s 278s test-bcf-sr: 278s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/GNNswgrs3l -s 85644070 278s .. ok 278s 278s test-bcf-sr: 278s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/GNNswgrs3l -s 49879942 278s .. ok 278s 278s test-bcf-sr: 278s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/GNNswgrs3l -s 47881429 278s .. ok 278s 278s test-bcf-sr: 278s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/GNNswgrs3l -s 69081244 279s .. ok 279s 279s test-bcf-sr: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/GNNswgrs3l -s 83459376 279s .. ok 279s 279s test_bcf_sr_no_index: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/bcf-sr/merge.noidx.b.vcf /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/GNNswgrs3l/no_index_1.err 279s .. ok 279s 279s test_bcf_sr_no_index: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/GNNswgrs3l/no_index_2.out 2> /tmp/GNNswgrs3l/no_index_2.err (expected fail) 279s .. ok 279s 279s test_bcf_sr_no_index: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/GNNswgrs3l/no_index_3.out 2> /tmp/GNNswgrs3l/no_index_3.err (expected fail) 279s .. ok 279s 279s test_bcf_sr_no_index: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf > /tmp/GNNswgrs3l/no_index_4.out 2> /tmp/GNNswgrs3l/no_index_4.err (expected fail) 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -b -p /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf -x /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf.csi /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/bcf-sr/weird-chr-names.vcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_1.out.vcf -r '1' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_2.out.vcf -r '1:1-2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_4.out.vcf -r '1:1-1' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_5.out.vcf -r '{1:1}' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf (expected fail) 279s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 279s Failed to set regions 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_14.out.vcf -t '1' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_15.out.vcf -t '1:1-2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_17.out.vcf -t '1:1-1' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_18.out.vcf -t '{1:1}' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf 279s .. ok 279s 279s test_bcf_sr_range: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/GNNswgrs3l/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/GNNswgrs3l/weird-chr-names.vcf.bcf (expected fail) 279s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 279s Failed to set targets 279s .. ok 279s 279s test_command: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf-translate - 279s .. ok 279s 279s test_convert_padded_header: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/GNNswgrs3l/headernul0.bam 279s .. ok 279s 279s test_convert_padded_header: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/GNNswgrs3l/headernul1.bam 279s .. ok 279s 279s test_convert_padded_header: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/GNNswgrs3l/headernul678.bam 279s .. ok 279s 279s test_rebgzip: Alternate zlib/deflate library detected 279s test_rebgzip: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/bgzip -I /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/bgziptest.txt.tmp.gz.gzi -c -g /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/bgziptest.txt 279s .. ok 279s 279s test-logging: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-logging.pl 279s .. ok 279s 279s test_plugin_loading: 279s HTS_PATH=/tmp/autopkgtest.T4wPj3/autopkgtest_tmp /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/with-shlib.sh /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/htsfile https://localhost:99999/invalid_port 279s .. ok 279s 279s test_realn: 279s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn01.sam -o - 280s .. ok 280s 280s test_realn: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn02.sam -o - 280s .. ok 280s 280s test_realn: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn01.sam -o - 280s .. ok 280s 280s test_realn: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn02.sam -o - 280s .. ok 280s 280s test_realn: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn01.sam -o - 280s .. ok 280s 280s test_realn: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn02.sam -o - 280s .. ok 280s 280s test_realn: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_realn -r -f /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn02-r.sam -o - 280s .. ok 280s 280s test_realn: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn02_exp.sam -o - 280s .. ok 280s 280s test_realn: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn02_exp-a.sam -o - 280s .. ok 280s 280s test_realn: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn03.fa -e -i /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/realn03.sam -o - 280s .. ok 280s 280s test-bcf_set_variant_type: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/test-bcf_set_variant_type 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -c chr,beg,end -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -c chr,beg,end -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -c chr,beg,end -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl,value:overlap,value -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl,value:overlap,value -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl,value:overlap,value -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -O 0.5 -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -O 0.5 -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -O 0.5 -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -rO 0.5 -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -rO 0.5 -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -rO 0.5 -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.1.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.2.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -a nbp,frac -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.3.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.3.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.3.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -a nbp,frac -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.3.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.3.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl:overlap -a nbp,frac -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.3.txt 280s .. ok 280s 280s run_annot_tsv: 280s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.4.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.4.txt 280s .. ok 280s 280s run_annot_tsv: 280s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.4.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.4.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.4.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.4.txt 281s .. ok 281s 281s run_annot_tsv: 281s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.5.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.5.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.5.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.5.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.5.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.5.txt 281s .. ok 281s 281s run_annot_tsv: 281s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.6.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.6.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.6.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.6.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.6.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.6.txt 281s .. ok 281s 281s run_annot_tsv: 281s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.7.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.7.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.7.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.7.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.7.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.7.txt 281s .. ok 281s 281s run_annot_tsv: 281s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.8.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.8.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.8.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.8.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.8.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.8.txt 281s .. ok 281s 281s run_annot_tsv: 281s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.9.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.9.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.9.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.9.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.9.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.9.txt 281s .. ok 281s 281s run_annot_tsv: 281s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -f smpl -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt 281s .. ok 281s 281s run_annot_tsv: 281s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt 281s .. ok 281s 281s run_annot_tsv: 281s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -x -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -x -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -x -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt 281s .. ok 281s 281s run_annot_tsv: 281s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -m smpl -f smpl -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt 281s .. ok 281s 281s run_annot_tsv: 281s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -m smpl -f smpl -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt 282s .. ok 282s 282s run_annot_tsv: 282s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -m smpl -f smpl -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt 282s .. ok 282s 282s run_annot_tsv: 282s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -m smpl -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt 282s .. ok 282s 282s run_annot_tsv: 282s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -m smpl -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt 282s .. ok 282s 282s run_annot_tsv: 282s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -m smpl -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt 282s .. ok 282s 282s run_annot_tsv: 282s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -m smpl -x -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt 282s .. ok 282s 282s run_annot_tsv: 282s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -m smpl -x -s /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt 282s .. ok 282s 282s run_annot_tsv: 282s cat /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/annot-tsv -m smpl -x -t /tmp/autopkgtest.T4wPj3/autopkgtest_tmp/test/annot-tsv/dst.10.txt 282s .. ok 282s 282s 282s Number of tests: 282s total .. 291 282s passed .. 291 282s failed .. 0 282s 282s + echo PASS 282s PASS 282s autopkgtest [17:16:20]: test run-unit-test: -----------------------] 283s run-unit-test PASS 283s autopkgtest [17:16:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 283s autopkgtest [17:16:21]: @@@@@@@@@@@@@@@@@@@@ summary 283s run-unit-test PASS 302s Creating nova instance adt-noble-arm64-htslib-20240316-171138-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...