0s autopkgtest [09:12:05]: starting date and time: 2024-11-13 09:12:05+0000 0s autopkgtest [09:12:05]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [09:12:05]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hw_0qw_n/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade parallel-fastq-dump --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-18.secgroup --name adt-plucky-amd64-parallel-fastq-dump-20241113-091205-juju-7f2275-prod-proposed-migration-environment-2-96382bf3-3174-4304-8742-bda689abdd16 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -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,keyserver.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/ 56s autopkgtest [09:13:01]: testbed dpkg architecture: amd64 56s autopkgtest [09:13:01]: testbed apt version: 2.9.8 56s autopkgtest [09:13:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 57s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 57s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 57s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 57s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 59s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 59s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 59s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 59s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 59s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 59s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 60s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 60s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 61s Fetched 2173 kB in 4s (584 kB/s) 61s Reading package lists... 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Calculating upgrade... 63s The following NEW packages will be installed: 63s python3.13-gdbm 63s The following packages will be upgraded: 63s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 64s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 64s Need to get 253 kB of archives. 64s After this operation, 147 kB of additional disk space will be used. 64s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 64s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 64s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 64s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 64s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 64s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 64s Fetched 253 kB in 1s (399 kB/s) 64s (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 ... 75541 files and directories currently installed.) 64s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 64s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 64s Setting up python3-minimal (3.12.7-1) ... 65s (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 ... 75541 files and directories currently installed.) 65s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 65s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 65s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 65s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 65s Selecting previously unselected package python3.13-gdbm. 65s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 65s Unpacking python3.13-gdbm (3.13.0-2) ... 65s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 65s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 65s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 65s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 65s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 65s Setting up python3.13-gdbm (3.13.0-2) ... 65s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 65s Setting up python3 (3.12.7-1) ... 65s Setting up python3-gdbm:amd64 (3.12.7-1) ... 65s Processing triggers for man-db (2.12.1-3) ... 65s Processing triggers for libc-bin (2.40-1ubuntu3) ... 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 66s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 67s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 67s Reading package lists... 67s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Calculating upgrade... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s autopkgtest [09:13:16]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 71s autopkgtest [09:13:16]: @@@@@@@@@@@@@@@@@@@@ apt-source parallel-fastq-dump 72s Get:1 http://ftpmaster.internal/ubuntu plucky/universe parallel-fastq-dump 0.6.7-3 (dsc) [2141 B] 72s Get:2 http://ftpmaster.internal/ubuntu plucky/universe parallel-fastq-dump 0.6.7-3 (tar) [4208 B] 72s Get:3 http://ftpmaster.internal/ubuntu plucky/universe parallel-fastq-dump 0.6.7-3 (diff) [3080 B] 72s gpgv: Signature made Tue Mar 29 18:39:12 2022 UTC 72s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 72s gpgv: issuer "nilesh@debian.org" 72s gpgv: Can't check signature: No public key 72s dpkg-source: warning: cannot verify inline signature for ./parallel-fastq-dump_0.6.7-3.dsc: no acceptable signature found 72s autopkgtest [09:13:17]: testing package parallel-fastq-dump version 0.6.7-3 73s autopkgtest [09:13:18]: build not needed 73s autopkgtest [09:13:18]: test run-unit-test: preparing testbed 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Starting pkgProblemResolver with broken count: 0 74s Starting 2 pkgProblemResolver with broken count: 0 74s Done 75s The following additional packages will be installed: 75s libabsl20230802 libaec0 libhdf5-103-1t64 libmbedcrypto16 libmbedtls21 75s libmbedx509-7 libncbi-vdb3 libncbi-wvdb3 libre2-11 libsz2 ncbi-vdb-data 75s parallel-fastq-dump sra-toolkit 75s Recommended packages: 75s med-config 75s The following NEW packages will be installed: 75s autopkgtest-satdep libabsl20230802 libaec0 libhdf5-103-1t64 libmbedcrypto16 75s libmbedtls21 libmbedx509-7 libncbi-vdb3 libncbi-wvdb3 libre2-11 libsz2 75s ncbi-vdb-data parallel-fastq-dump sra-toolkit 75s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 75s Need to get 12.4 MB/12.4 MB of archives. 75s After this operation, 34.2 MB of additional disk space will be used. 75s Get:1 /tmp/autopkgtest.croVz8/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 75s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libabsl20230802 amd64 20230802.1-4ubuntu1 [499 kB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 76s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 76s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 78s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto16 amd64 3.6.2-2ubuntu1 [275 kB] 78s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-7 amd64 3.6.2-2ubuntu1 [37.1 kB] 78s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls21 amd64 3.6.2-2ubuntu1 [126 kB] 79s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [67.7 kB] 79s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1409 kB] 81s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-wvdb3 amd64 3.0.9+dfsg-2 [1417 kB] 82s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libre2-11 amd64 20240501-3build1 [166 kB] 82s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 sra-toolkit amd64 3.0.3+dfsg-9ubuntu1 [7055 kB] 92s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 parallel-fastq-dump amd64 0.6.7-3 [5632 B] 92s Fetched 12.4 MB in 17s (719 kB/s) 92s Selecting previously unselected package libabsl20230802:amd64. 92s (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 ... 75548 files and directories currently installed.) 92s Preparing to unpack .../00-libabsl20230802_20230802.1-4ubuntu1_amd64.deb ... 92s Unpacking libabsl20230802:amd64 (20230802.1-4ubuntu1) ... 92s Selecting previously unselected package libaec0:amd64. 92s Preparing to unpack .../01-libaec0_1.1.3-1_amd64.deb ... 92s Unpacking libaec0:amd64 (1.1.3-1) ... 92s Selecting previously unselected package libsz2:amd64. 92s Preparing to unpack .../02-libsz2_1.1.3-1_amd64.deb ... 92s Unpacking libsz2:amd64 (1.1.3-1) ... 92s Selecting previously unselected package libhdf5-103-1t64:amd64. 92s Preparing to unpack .../03-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 92s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 92s Selecting previously unselected package libmbedcrypto16:amd64. 92s Preparing to unpack .../04-libmbedcrypto16_3.6.2-2ubuntu1_amd64.deb ... 92s Unpacking libmbedcrypto16:amd64 (3.6.2-2ubuntu1) ... 92s Selecting previously unselected package libmbedx509-7:amd64. 92s Preparing to unpack .../05-libmbedx509-7_3.6.2-2ubuntu1_amd64.deb ... 92s Unpacking libmbedx509-7:amd64 (3.6.2-2ubuntu1) ... 92s Selecting previously unselected package libmbedtls21:amd64. 92s Preparing to unpack .../06-libmbedtls21_3.6.2-2ubuntu1_amd64.deb ... 92s Unpacking libmbedtls21:amd64 (3.6.2-2ubuntu1) ... 92s Selecting previously unselected package ncbi-vdb-data. 92s Preparing to unpack .../07-ncbi-vdb-data_3.0.9+dfsg-2_all.deb ... 92s Unpacking ncbi-vdb-data (3.0.9+dfsg-2) ... 92s Selecting previously unselected package libncbi-vdb3:amd64. 92s Preparing to unpack .../08-libncbi-vdb3_3.0.9+dfsg-2_amd64.deb ... 92s Unpacking libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... 92s Selecting previously unselected package libncbi-wvdb3:amd64. 92s Preparing to unpack .../09-libncbi-wvdb3_3.0.9+dfsg-2_amd64.deb ... 92s Unpacking libncbi-wvdb3:amd64 (3.0.9+dfsg-2) ... 92s Selecting previously unselected package libre2-11:amd64. 92s Preparing to unpack .../10-libre2-11_20240501-3build1_amd64.deb ... 92s Unpacking libre2-11:amd64 (20240501-3build1) ... 92s Selecting previously unselected package sra-toolkit. 92s Preparing to unpack .../11-sra-toolkit_3.0.3+dfsg-9ubuntu1_amd64.deb ... 92s Unpacking sra-toolkit (3.0.3+dfsg-9ubuntu1) ... 93s Selecting previously unselected package parallel-fastq-dump. 93s Preparing to unpack .../12-parallel-fastq-dump_0.6.7-3_amd64.deb ... 93s Unpacking parallel-fastq-dump (0.6.7-3) ... 93s Selecting previously unselected package autopkgtest-satdep. 93s Preparing to unpack .../13-1-autopkgtest-satdep.deb ... 93s Unpacking autopkgtest-satdep (0) ... 93s Setting up libaec0:amd64 (1.1.3-1) ... 93s Setting up ncbi-vdb-data (3.0.9+dfsg-2) ... 93s Setting up libabsl20230802:amd64 (20230802.1-4ubuntu1) ... 93s Setting up libmbedcrypto16:amd64 (3.6.2-2ubuntu1) ... 93s Setting up libsz2:amd64 (1.1.3-1) ... 93s Setting up libre2-11:amd64 (20240501-3build1) ... 93s Setting up libmbedx509-7:amd64 (3.6.2-2ubuntu1) ... 93s Setting up libmbedtls21:amd64 (3.6.2-2ubuntu1) ... 93s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 93s Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... 93s Setting up libncbi-wvdb3:amd64 (3.0.9+dfsg-2) ... 93s Setting up sra-toolkit (3.0.3+dfsg-9ubuntu1) ... 93s Setting up parallel-fastq-dump (0.6.7-3) ... 93s Setting up autopkgtest-satdep (0) ... 93s Processing triggers for libc-bin (2.40-1ubuntu3) ... 95s (Reading database ... 75930 files and directories currently installed.) 95s Removing autopkgtest-satdep (0) ... 95s autopkgtest [09:13:40]: test run-unit-test: [----------------------- 96s 2024-11-13 09:13:41,084 - SRR ids: ['SRR014849'] 96s 2024-11-13 09:13:41,084 - extra args: ['--split-files', '--gzip'] 96s 2024-11-13 09:13:41,084 - tempdir: /tmp/pfd_vo1_dzz_ 96s 2024-11-13 09:13:41,084 - CMD: sra-stat --meta --quick SRR014849 219s Traceback (most recent call last): 219s File "/usr/bin/parallel-fastq-dump", line 116, in get_spot_count 219s total += int(l.split('|')[2].split(':')[0]) 219s ~~~~~~~~~~~~^^^ 219s IndexError: list index out of range 219s 219s During handling of the above exception, another exception occurred: 219s 219s Traceback (most recent call last): 219s File "/usr/bin/parallel-fastq-dump", line 181, in 219s main() 219s File "/usr/bin/parallel-fastq-dump", line 175, in main 219s pfd(args, si, extra_args) 219s File "/usr/bin/parallel-fastq-dump", line 49, in pfd 219s n_spots = get_spot_count(srr_id) 219s ^^^^^^^^^^^^^^^^^^^^^^ 219s File "/usr/bin/parallel-fastq-dump", line 122, in get_spot_count 219s raise IndexError(msg.format('\n'.join(txt), '\n'.join(etxt))) 219s IndexError: sra-stat output parsing error! 219s --sra-stat STDOUT-- 219s 219s --sra-stat STDERR-- 219s 2024-11-13T09:15:43 sra-stat.3.0.3 int: directory not found while opening manager within virtual file system module - 'SRR014849' 220s autopkgtest [09:15:45]: test run-unit-test: -----------------------] 220s autopkgtest [09:15:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 220s run-unit-test FAIL non-zero exit status 1 220s autopkgtest [09:15:45]: @@@@@@@@@@@@@@@@@@@@ summary 220s run-unit-test FAIL non-zero exit status 1 225s virt: nova [W] Skipping flock for amd64 225s virt: Creating nova instance adt-plucky-amd64-parallel-fastq-dump-20241113-091205-juju-7f2275-prod-proposed-migration-environment-2-96382bf3-3174-4304-8742-bda689abdd16 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...