0s autopkgtest [17:48:09]: starting date and time: 2024-03-24 17:48:09+0000 0s autopkgtest [17:48:09]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:48:09]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.l_g6fs_6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade nanosv --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-arm64-16.secgroup --name adt-noble-arm64-nanosv-20240324-173325-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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://us.ports.ubuntu.com/ubuntu-ports/ 141s autopkgtest [17:50:30]: testbed dpkg architecture: arm64 141s autopkgtest [17:50:30]: testbed apt version: 2.7.12 141s autopkgtest [17:50:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 142s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 142s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 142s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 142s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 143s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 143s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [710 kB] 143s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 143s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 143s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 143s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 143s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 143s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 143s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 149s Fetched 9851 kB in 3s (3397 kB/s) 149s Reading package lists... 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 154s Calculating upgrade... 155s The following packages will be REMOVED: 155s libssl3 155s The following NEW packages will be installed: 155s libssl3t64 155s The following packages have been kept back: 155s curl 155s The following packages will be upgraded: 155s openssl 156s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 156s Need to get 2777 kB of archives. 156s After this operation, 139 kB of additional disk space will be used. 156s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 156s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 157s Fetched 2777 kB in 1s (3940 kB/s) 157s (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 ... 75911 files and directories currently installed.) 157s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 157s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 157s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 157s wget depends on libssl3 (>= 3.0.0). 157s u-boot-tools depends on libssl3 (>= 3.0.0). 157s tnftp depends on libssl3 (>= 3.0.0). 157s tcpdump depends on libssl3 (>= 3.0.0). 157s systemd-resolved depends on libssl3 (>= 3.0.0). 157s systemd depends on libssl3 (>= 3.0.0). 157s sudo depends on libssl3 (>= 3.0.0). 157s sbsigntool depends on libssl3 (>= 3.0.0). 157s rsync depends on libssl3 (>= 3.0.0). 157s python3-cryptography depends on libssl3 (>= 3.0.0). 157s openssh-server depends on libssl3 (>= 3.0.10). 157s openssh-client depends on libssl3 (>= 3.0.10). 157s mtd-utils depends on libssl3 (>= 3.0.0). 157s mokutil depends on libssl3 (>= 3.0.0). 157s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 157s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 157s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 157s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 157s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 157s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 157s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 157s libnvme1 depends on libssl3 (>= 3.0.0). 157s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 157s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 157s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 157s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 157s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 157s kmod depends on libssl3 (>= 3.0.0). 157s dhcpcd-base depends on libssl3 (>= 3.0.0). 157s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 157s 157s (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 ... 75911 files and directories currently installed.) 157s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 157s Selecting previously unselected package libssl3t64:arm64. 158s (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 ... 75900 files and directories currently installed.) 158s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 158s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 158s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 158s Setting up openssl (3.0.13-0ubuntu2) ... 158s Processing triggers for man-db (2.12.0-3) ... 158s Processing triggers for libc-bin (2.39-0ubuntu6) ... 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 161s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 162s sh: Attempting to set up Debian/Ubuntu apt sources automatically 162s sh: Distribution appears to be Ubuntu 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 165s eatmydata is already the newest version (131-1). 165s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s Reading package lists... 166s Building dependency tree... 166s Reading state information... 167s dbus is already the newest version (1.14.10-4ubuntu1). 167s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s Reading package lists... 167s Building dependency tree... 167s Reading state information... 169s rng-tools-debian is already the newest version (2.4). 169s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 170s The following packages will be REMOVED: 170s cloud-init* python3-configobj* python3-debconf* 171s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 171s After this operation, 3256 kB disk space will be freed. 171s (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 ... 75913 files and directories currently installed.) 171s Removing cloud-init (24.1.2-0ubuntu1) ... 172s Removing python3-configobj (5.0.8-3) ... 172s Removing python3-debconf (1.5.86) ... 173s Processing triggers for man-db (2.12.0-3) ... 173s (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 ... 75524 files and directories currently installed.) 173s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 174s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 175s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 175s invoke-rc.d: policy-rc.d denied execution of try-restart. 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 176s linux-generic is already the newest version (6.8.0-11.11+1). 176s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 177s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 177s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 182s Reading package lists... 182s Reading package lists... 183s Building dependency tree... 183s Reading state information... 184s Calculating upgrade... 185s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 185s Reading package lists... 185s Building dependency tree... 185s Reading state information... 186s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 187s autopkgtest [17:51:15]: rebooting testbed after setup commands that affected boot 341s autopkgtest [17:53:50]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 344s autopkgtest [17:53:53]: @@@@@@@@@@@@@@@@@@@@ apt-source nanosv 347s Get:1 http://ftpmaster.internal/ubuntu noble/universe nanosv 1.2.4+git20190409.c1ae30c-6 (dsc) [2202 B] 347s Get:2 http://ftpmaster.internal/ubuntu noble/universe nanosv 1.2.4+git20190409.c1ae30c-6 (tar) [2895 kB] 347s Get:3 http://ftpmaster.internal/ubuntu noble/universe nanosv 1.2.4+git20190409.c1ae30c-6 (diff) [4472 B] 347s gpgv: Signature made Sun Oct 24 22:09:09 2021 UTC 347s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 347s gpgv: issuer "nilesh@debian.org" 347s gpgv: Can't check signature: No public key 347s dpkg-source: warning: cannot verify inline signature for ./nanosv_1.2.4+git20190409.c1ae30c-6.dsc: no acceptable signature found 348s autopkgtest [17:53:57]: testing package nanosv version 1.2.4+git20190409.c1ae30c-6 349s autopkgtest [17:53:58]: build not needed 350s autopkgtest [17:53:59]: test run-unit-test: preparing testbed 356s Reading package lists... 357s Building dependency tree... 357s Reading state information... 357s Starting pkgProblemResolver with broken count: 0 358s Starting 2 pkgProblemResolver with broken count: 0 358s Done 359s The following additional packages will be installed: 359s bedtools libdeflate0 libhts3 libhtscodecs2 libphobos2-ldc-shared106 nanosv 359s python3-pysam python3-vcf sambamba samtools 359s Suggested packages: 359s cwltool 359s The following NEW packages will be installed: 359s autopkgtest-satdep bedtools libdeflate0 libhts3 libhtscodecs2 359s libphobos2-ldc-shared106 nanosv python3-pysam python3-vcf sambamba samtools 359s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 359s Need to get 12.3 MB/12.3 MB of archives. 359s After this operation, 74.6 MB of additional disk space will be used. 359s Get:1 /tmp/autopkgtest.pfLAxK/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 359s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 bedtools arm64 2.31.1+dfsg-2 [636 kB] 360s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 360s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 360s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 360s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libphobos2-ldc-shared106 arm64 1:1.36.0-2 [1276 kB] 360s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 360s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-vcf arm64 0.6.8+git20170215.476169c-10 [53.8 kB] 360s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 nanosv all 1.2.4+git20190409.c1ae30c-6 [4149 kB] 360s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 sambamba arm64 1.0.1+dfsg-1build3 [627 kB] 360s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 361s Fetched 12.3 MB in 1s (9771 kB/s) 361s Selecting previously unselected package bedtools. 361s (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 ... 75469 files and directories currently installed.) 361s Preparing to unpack .../00-bedtools_2.31.1+dfsg-2_arm64.deb ... 361s Unpacking bedtools (2.31.1+dfsg-2) ... 361s Selecting previously unselected package libdeflate0:arm64. 361s Preparing to unpack .../01-libdeflate0_1.19-1_arm64.deb ... 361s Unpacking libdeflate0:arm64 (1.19-1) ... 361s Selecting previously unselected package libhtscodecs2:arm64. 361s Preparing to unpack .../02-libhtscodecs2_1.6.0-1_arm64.deb ... 361s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 361s Selecting previously unselected package libhts3:arm64. 361s Preparing to unpack .../03-libhts3_1.18+ds-1_arm64.deb ... 361s Unpacking libhts3:arm64 (1.18+ds-1) ... 361s Selecting previously unselected package libphobos2-ldc-shared106:arm64. 361s Preparing to unpack .../04-libphobos2-ldc-shared106_1%3a1.36.0-2_arm64.deb ... 361s Unpacking libphobos2-ldc-shared106:arm64 (1:1.36.0-2) ... 361s Selecting previously unselected package python3-pysam. 361s Preparing to unpack .../05-python3-pysam_0.22.0+ds-1_arm64.deb ... 361s Unpacking python3-pysam (0.22.0+ds-1) ... 362s Selecting previously unselected package python3-vcf. 362s Preparing to unpack .../06-python3-vcf_0.6.8+git20170215.476169c-10_arm64.deb ... 362s Unpacking python3-vcf (0.6.8+git20170215.476169c-10) ... 362s Selecting previously unselected package nanosv. 362s Preparing to unpack .../07-nanosv_1.2.4+git20190409.c1ae30c-6_all.deb ... 362s Unpacking nanosv (1.2.4+git20190409.c1ae30c-6) ... 362s Selecting previously unselected package sambamba. 362s Preparing to unpack .../08-sambamba_1.0.1+dfsg-1build3_arm64.deb ... 362s Unpacking sambamba (1.0.1+dfsg-1build3) ... 362s Selecting previously unselected package samtools. 362s Preparing to unpack .../09-samtools_1.19.2-1_arm64.deb ... 362s Unpacking samtools (1.19.2-1) ... 362s Selecting previously unselected package autopkgtest-satdep. 362s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 362s Unpacking autopkgtest-satdep (0) ... 362s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 362s Setting up libdeflate0:arm64 (1.19-1) ... 362s Setting up libphobos2-ldc-shared106:arm64 (1:1.36.0-2) ... 362s Setting up bedtools (2.31.1+dfsg-2) ... 362s Setting up libhts3:arm64 (1.18+ds-1) ... 362s Setting up python3-pysam (0.22.0+ds-1) ... 363s Setting up sambamba (1.0.1+dfsg-1build3) ... 363s Setting up samtools (1.19.2-1) ... 363s Setting up python3-vcf (0.6.8+git20170215.476169c-10) ... 363s /usr/lib/python3/dist-packages/vcf/parser.py:278: SyntaxWarning: invalid escape sequence '\[' 363s self._alt_pattern = re.compile('[\[\]]') 363s /usr/lib/python3/dist-packages/vcf/parser.py:536: SyntaxWarning: invalid escape sequence '\[' 363s remoteOrientation = (re.search('\[', str) is not None) 363s Setting up nanosv (1.2.4+git20190409.c1ae30c-6) ... 363s /usr/lib/python3/dist-packages/nanosv/utils/parse_bam.py:43: SyntaxWarning: invalid escape sequence '\.' 363s sample_name = re.sub('(\.sorted)?\.bam$', '', str(NanoSV.opts_bam)) 363s /usr/lib/python3/dist-packages/nanosv/utils/parse_bam.py:206: SyntaxWarning: invalid escape sequence '\d' 363s pattern_list[i] += '[' + str(int(NanoSV.opts_min_indel_size[i]) + 1) + '-9]\d{' + str(j) + ',}' 363s /usr/lib/python3/dist-packages/nanosv/utils/parse_bam.py:210: SyntaxWarning: invalid escape sequence '\d' 363s pattern_list.append("\d{" + str(len(NanoSV.opts_min_indel_size) + 1) + ",}") 363s /usr/lib/python3/dist-packages/nanosv/utils/parse_bam.py:392: SyntaxWarning: invalid escape sequence '\^' 363s md_tag = re.split("\^\D+", md) 363s /usr/lib/python3/dist-packages/nanosv/utils/parse_bam.py:416: SyntaxWarning: invalid escape sequence '\D' 363s if re.search("\D+", md_tag[md_cursor]): 363s /usr/lib/python3/dist-packages/nanosv/utils/parse_bam.py:418: SyntaxWarning: invalid escape sequence '\D' 363s for m in re.split("\D", md_tag[md_cursor]): 363s Setting up autopkgtest-satdep (0) ... 363s Processing triggers for man-db (2.12.0-3) ... 364s Processing triggers for libc-bin (2.39-0ubuntu6) ... 369s (Reading database ... 76087 files and directories currently installed.) 369s Removing autopkgtest-satdep (0) ... 370s autopkgtest [17:54:19]: test run-unit-test: [----------------------- 370s Sun Mar 24 17:54:20 2024 Busy with calculating the coverage distribution... 370s Sun Mar 24 17:54:20 2024 Busy with parsing bam file... 381s Sun Mar 24 17:54:30 2024 Busy with parsing read segments... 381s Sun Mar 24 17:54:30 2024 Busy with parsing breakpoints... 381s Sun Mar 24 17:54:30 2024 Busy with reference reads... 381s Sun Mar 24 17:54:30 2024 Busy with printing to vcf... 381s PASS Test 381s autopkgtest [17:54:30]: test run-unit-test: -----------------------] 382s run-unit-test PASS 382s autopkgtest [17:54:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 382s autopkgtest [17:54:31]: @@@@@@@@@@@@@@@@@@@@ summary 382s run-unit-test PASS 398s Creating nova instance adt-noble-arm64-nanosv-20240324-173325-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...