0s autopkgtest [17:53:08]: starting date and time: 2025-03-15 17:53:08+0000 0s autopkgtest [17:53:08]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:53:08]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.jgiskebf/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade subread --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.141 lxd-armhf-10.145.243.141:autopkgtest/ubuntu/plucky/armhf 22s autopkgtest [17:53:30]: testbed dpkg architecture: armhf 24s autopkgtest [17:53:32]: testbed apt version: 2.9.33 28s autopkgtest [17:53:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [17:53:38]: testbed release detected to be: None 38s autopkgtest [17:53:46]: updating testbed package index (apt update) 40s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 40s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 41s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 41s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 41s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 41s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 41s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 41s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 42s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 42s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 42s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 42s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 42s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 42s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 42s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 44s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 67s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 68s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 69s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 69s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 69s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 87s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 89s Fetched 41.0 MB in 49s (839 kB/s) 91s Reading package lists... 97s autopkgtest [17:54:45]: upgrading testbed (apt dist-upgrade and autopurge) 98s Reading package lists... 99s Building dependency tree... 99s Reading state information... 100s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 100s Starting 2 pkgProblemResolver with broken count: 0 100s Done 101s Entering ResolveByKeep 101s 102s Calculating upgrade... 103s The following packages will be upgraded: 103s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 103s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s Need to get 8683 kB of archives. 103s After this operation, 23.6 kB of additional disk space will be used. 103s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 106s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 110s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 111s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 111s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 111s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 112s Preconfiguring packages ... 112s Fetched 8683 kB in 8s (1031 kB/s) 112s (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 ... 64655 files and directories currently installed.) 112s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 112s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Setting up libc6:armhf (2.41-1ubuntu2) ... 113s (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 ... 64655 files and directories currently installed.) 113s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 113s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Setting up libc-bin (2.41-1ubuntu2) ... 114s (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 ... 64655 files and directories currently installed.) 114s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 114s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 114s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 114s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 114s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 114s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 114s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 114s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 114s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 115s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 115s Setting up sos (4.9.0-5) ... 116s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 116s Setting up locales (2.41-1ubuntu2) ... 118s Generating locales (this might take a while)... 124s en_US.UTF-8... done 124s Generation complete. 124s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 124s Setting up strace (6.13+ds-1ubuntu1) ... 124s Processing triggers for man-db (2.13.0-1) ... 126s Processing triggers for systemd (257.3-1ubuntu3) ... 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s Starting pkgProblemResolver with broken count: 0 130s Starting 2 pkgProblemResolver with broken count: 0 130s Done 131s Solving dependencies... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s autopkgtest [17:55:22]: rebooting testbed after setup commands that affected boot 182s autopkgtest [17:56:10]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 207s autopkgtest [17:56:35]: @@@@@@@@@@@@@@@@@@@@ apt-source subread 237s Get:1 http://ftpmaster.internal/ubuntu plucky/universe subread 2.0.7+dfsg-1 (dsc) [2332 B] 237s Get:2 http://ftpmaster.internal/ubuntu plucky/universe subread 2.0.7+dfsg-1 (tar) [16.5 MB] 237s Get:3 http://ftpmaster.internal/ubuntu plucky/universe subread 2.0.7+dfsg-1 (diff) [19.6 kB] 238s gpgv: Signature made Sat Aug 31 10:04:54 2024 UTC 238s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 238s gpgv: issuer "emollier@debian.org" 238s gpgv: Can't check signature: No public key 238s dpkg-source: warning: cannot verify inline signature for ./subread_2.0.7+dfsg-1.dsc: no acceptable signature found 239s autopkgtest [17:57:07]: testing package subread version 2.0.7+dfsg-1 241s autopkgtest [17:57:09]: build not needed 245s autopkgtest [17:57:13]: test subread-tests: preparing testbed 247s Reading package lists... 248s Building dependency tree... 248s Reading state information... 248s Starting pkgProblemResolver with broken count: 0 248s Starting 2 pkgProblemResolver with broken count: 0 248s Done 250s The following NEW packages will be installed: 250s subread subread-data 250s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 250s Need to get 19.9 MB of archives. 250s After this operation, 25.3 MB of additional disk space will be used. 250s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf subread armhf 2.0.7+dfsg-1 [723 kB] 250s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf subread-data all 2.0.7+dfsg-1 [19.2 MB] 268s Fetched 19.9 MB in 18s (1101 kB/s) 268s Selecting previously unselected package subread. 268s (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 ... 64655 files and directories currently installed.) 268s Preparing to unpack .../subread_2.0.7+dfsg-1_armhf.deb ... 268s Unpacking subread (2.0.7+dfsg-1) ... 268s Selecting previously unselected package subread-data. 269s Preparing to unpack .../subread-data_2.0.7+dfsg-1_all.deb ... 269s Unpacking subread-data (2.0.7+dfsg-1) ... 269s Setting up subread (2.0.7+dfsg-1) ... 269s Setting up subread-data (2.0.7+dfsg-1) ... 269s Processing triggers for man-db (2.13.0-1) ... 279s autopkgtest [17:57:47]: test subread-tests: [----------------------- 282s  282s 282s 282s 282s ************************************************** 282s ************************************************** 282s *** *** 282s *** This script will test the major functions *** 282s *** in our package, including the index build- *** 282s *** er, subread-align, subjunc, featureCounts *** 282s *** and exactSNP. *** 282s *** *** 282s *** Test will start in seconds. *** 282s *** *** 282s ************************************************** 282s ************************************************** 282s 283s 9test_all.sh: line 25: bc: command not found 284s test_all.sh: line 25: bc: command not found 285s test_all.sh: line 25: bc: command not found 286s test_all.sh: line 25: bc: command not found 287s test_all.sh: line 25: bc: command not found 288s test_all.sh: line 25: bc: command not found 289s test_all.sh: line 25: bc: command not found 290s test_all.sh: line 25: bc: command not found 291s test_all.sh: line 25: bc: command not found 291s [0,0Hrm: cannot remove 'test-tmp.log': No such file or directory 291s 291s ========== _____ _ _ ____ _____ ______ _____ 291s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 291s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 291s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 291s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 291s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 291s v2.0.7 291s 291s //================================= setting ==================================\\ 291s || || 291s || Index name : small1 || 291s || Index space : base space || 291s || Index split : no-split || 291s || Repeat threshold : 100 repeats || 291s || Gapped index : no || 291s || || 291s || Free / total memory : 0.2GB / 0.0GB || 291s || || 291s || Input files : 1 file in total || 291s || o chr901.fa || 291s || || 291s || || 291s || WARNING: the free memory is lower than 3.0GB. || 291s || the program may run very slow or crash. || 291s || || 291s \\============================================================================// 291s 291s //================================= Running ==================================\\ 291s || || 291s || Check the integrity of provided reference sequences ... || 291s || There were 4 notes for reference sequences. || 291s || The notes can be found in the log file, '../small1.log'. || 291s || Scan uninformative subreads in reference sequences ... || 293s subread-buildindex: hashtable.c:470: HashTablePutReplaceEx: Assertion `key != NULL' failed. 294s Aborted (core dumped) 294s md5sum: ../small1.00.b.array: No such file or directory 294s md5sum: ../small1.00.b.tab: No such file or directory 294s 294s ========== _____ _ _ ____ _____ ______ _____ 294s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 294s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 294s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 294s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 294s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 294s v2.0.7 294s 294s //================================= setting ==================================\\ 294s || || 294s || Function : Read alignment (RNA-Seq) || 294s || Input file : test-noerror-r1.fq || 294s || Output file : test-tmp.sam (SAM) || 294s || Index name : small1 || 294s || || 294s || ------------------------------------ || 294s || || 294s || Threads : 1 || 294s || Phred offset : 64 || 294s || Min votes : 3 / 10 || 294s || Max mismatches : 3 || 294s || Max indel length : 5 || 294s || Report multi-mapping reads : no || 294s || Max alignments per multi-mapping read : 1 || 294s || || 294s \\============================================================================// 294s 294s //================= Running (15-Mar-2025 17:58:01, pid=981) ==================\\ 294s || || 294s || Check the input reads. || 294s || The input file contains base space reads. || 294s || Initialise the memory objects. || 294s || Estimate the mean read length. || 294s || The range of Phred scores observed in the data is [9,9] || 294s || Create the output SAM file. || 294s || Check the index. || 294s Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix. 294s 294s Traceback (most recent call last): 294s File "/tmp/tmp.IMEgmk7sLf/test/subread-align/readname_ora_match.py", line 83, in 294s main() 294s ~~~~^^ 294s File "/tmp/tmp.IMEgmk7sLf/test/subread-align/readname_ora_match.py", line 80, in main 294s print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN)) 294s ~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~ 294s ZeroDivisionError: float division by zero 294s 294s ========== _____ _ _ ____ _____ ______ _____ 294s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 294s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 294s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 294s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 294s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 294s v2.0.7 294s 294s //================================= setting ==================================\\ 294s || || 294s || Function : Read alignment (RNA-Seq) || 294s || Input file : test-noerror-r1.fq || 294s || Output file : test-tmp.sam (SAM) || 294s || Index name : small1 || 294s || || 294s || ------------------------------------ || 294s || || 294s || Threads : 1 || 294s || Phred offset : 64 || 294s || Min votes : 3 / 10 || 294s || Max mismatches : 3 || 294s || Max indel length : 5 || 294s || Report multi-mapping reads : no || 294s || Max alignments per multi-mapping read : 1 || 294s || || 294s \\============================================================================// 294s 294s //================= Running (15-Mar-2025 17:58:02, pid=984) ==================\\ 294s || || 294s || Check the input reads. || 294s || The input file contains base space reads. || 294s || Initialise the memory objects. || 294s || Estimate the mean read length. || 294s || The range of Phred scores observed in the data is [9,9] || 294s || Create the output SAM file. || 294s || Check the index. || 294s Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix. 294s 294s Traceback (most recent call last): 294s File "/tmp/tmp.IMEgmk7sLf/test/subread-align/readname_ora_match.py", line 83, in 294s main() 294s ~~~~^^ 294s File "/tmp/tmp.IMEgmk7sLf/test/subread-align/readname_ora_match.py", line 80, in main 294s print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN)) 294s ~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~ 294s ZeroDivisionError: float division by zero 294s 294s ========== _____ _ _ ____ _____ ______ _____ 294s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 294s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 294s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 294s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 294s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 294s v2.0.7 294s 294s //================================= setting ==================================\\ 294s || || 294s || Function : Read alignment (RNA-Seq) || 294s || Input file 1 : test-noerror-r1.fq || 294s || Input file 2 : test-noerror-r2.fq || 294s || Output file : test-tmp.sam (SAM) || 294s || Index name : small1 || 294s || || 294s || ------------------------------------ || 294s || || 294s || Threads : 1 || 294s || Phred offset : 64 || 294s || # of extracted subreads : 10 || 294s || Min read1 vote : 3 || 294s || Min read2 vote : 1 || 294s || Max fragment size : 600 || 294s || Min fragment size : 50 || 294s || Max mismatches : 3 || 294s || Max indel length : 5 || 294s || Report multi-mapping reads : no || 294s || Max alignments per multi-mapping read : 1 || 294s || || 294s \\============================================================================// 294s 294s //================= Running (15-Mar-2025 17:58:02, pid=987) ==================\\ 294s || || 294s || Check the input reads. || 294s || The input file contains base space reads. || 294s || Initialise the memory objects. || 294s || Estimate the mean read length. || 294s || The range of Phred scores observed in the data is [9,9] || 294s || Create the output SAM file. || 294s || Check the index. || 294s Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix. 294s 294s Traceback (most recent call last): 294s File "/tmp/tmp.IMEgmk7sLf/test/subread-align/readname_ora_match.py", line 83, in 294s main() 294s ~~~~^^ 294s File "/tmp/tmp.IMEgmk7sLf/test/subread-align/readname_ora_match.py", line 80, in main 294s print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN)) 294s ~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~ 294s ZeroDivisionError: float division by zero 294s 294s ========== _____ _ _ ____ _____ ______ _____ 294s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 294s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 294s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 294s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 294s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 294s v2.0.7 294s 294s //================================= setting ==================================\\ 294s || || 294s || Function : Read alignment (RNA-Seq) || 294s || Input file 1 : test-noerror-r1.fq || 294s || Input file 2 : test-noerror-r2.fq || 294s || Output file : test-tmp.sam (SAM) || 294s || Index name : small1 || 294s || || 294s || ------------------------------------ || 294s || || 294s || Threads : 1 || 294s || Phred offset : 64 || 294s || # of extracted subreads : 10 || 294s || Min read1 vote : 3 || 294s || Min read2 vote : 1 || 294s || Max fragment size : 600 || 294s || Min fragment size : 50 || 294s || Max mismatches : 3 || 294s || Max indel length : 5 || 294s || Report multi-mapping reads : no || 294s || Max alignments per multi-mapping read : 1 || 294s || || 294s \\============================================================================// 294s 294s //================= Running (15-Mar-2025 17:58:02, pid=990) ==================\\ 294s || || 294s || Check the input reads. || 294s || The input file contains base space reads. || 294s || Initialise the memory objects. || 294s || Estimate the mean read length. || 294s || The range of Phred scores observed in the data is [9,9] || 294s || Create the output SAM file. || 294s || Check the index. || 294s Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix. 294s 294s Traceback (most recent call last): 294s File "/tmp/tmp.IMEgmk7sLf/test/subread-align/readname_ora_match.py", line 83, in 294s main() 294s ~~~~^^ 294s File "/tmp/tmp.IMEgmk7sLf/test/subread-align/readname_ora_match.py", line 80, in main 294s print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN)) 294s ~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~ 294s ZeroDivisionError: float division by zero 295s 295s ========== _____ _ _ ____ _____ ______ _____ 295s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 295s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 295s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 295s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 295s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 295s v2.0.7 295s 295s //================================= setting ==================================\\ 295s || || 295s || Function : Read alignment (RNA-Seq) || 295s || Input file 1 : test-error-r1.fq || 295s || Input file 2 : test-error-r2.fq || 295s || Output file : test-tmp.sam (SAM) || 295s || Index name : small1 || 295s || || 295s || ------------------------------------ || 295s || || 295s || Threads : 1 || 295s || Phred offset : 64 || 295s || # of extracted subreads : 10 || 295s || Min read1 vote : 3 || 295s || Min read2 vote : 1 || 295s || Max fragment size : 600 || 295s || Min fragment size : 50 || 295s || Max mismatches : 3 || 295s || Max indel length : 5 || 295s || Report multi-mapping reads : no || 295s || Max alignments per multi-mapping read : 1 || 295s || || 295s \\============================================================================// 295s 295s //================= Running (15-Mar-2025 17:58:03, pid=993) ==================\\ 295s || || 295s || Check the input reads. || 295s || The input file contains base space reads. || 295s || Initialise the memory objects. || 295s || Estimate the mean read length. || 295s || The range of Phred scores observed in the data is [-14,-14] || 295s || Create the output SAM file. || 295s || Check the index. || 295s Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix. 295s 295s Traceback (most recent call last): 295s File "/tmp/tmp.IMEgmk7sLf/test/subread-align/readname_ora_match.py", line 83, in 295s main() 295s ~~~~^^ 295s File "/tmp/tmp.IMEgmk7sLf/test/subread-align/readname_ora_match.py", line 80, in main 295s print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN)) 295s ~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~ 295s ZeroDivisionError: float division by zero 295s 295s ========== _____ _ _ ____ _____ ______ _____ 295s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 295s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 295s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 295s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 295s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 295s v2.0.7 295s 295s //================================= setting ==================================\\ 295s || || 295s || Function : Read alignment (RNA-Seq) || 295s || Input file 1 : test-err-mut-r1.fq.gz || 295s || Input file 2 : test-err-mut-r2.fq.gz || 295s || Output file : test-tmp.sam (SAM) || 295s || Index name : small1 || 295s || || 295s || ------------------------------------ || 295s || || 295s || Threads : 1 || 295s || Phred offset : 64 || 295s || # of extracted subreads : 10 || 295s || Min read1 vote : 3 || 295s || Min read2 vote : 1 || 295s || Max fragment size : 600 || 295s || Min fragment size : 50 || 295s || Max mismatches : 3 || 295s || Max indel length : 5 || 295s || Report multi-mapping reads : no || 295s || Max alignments per multi-mapping read : 1 || 295s || Read group name : MyTestGroup || 295s || || 295s \\============================================================================// 295s 295s //================= Running (15-Mar-2025 17:58:03, pid=996) ==================\\ 295s || || 295s ERROR: unable to open file 'data/test-err-mut-r1.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. 295s ERROR: unable to open file 'data/test-err-mut-r2.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. 295s Traceback (most recent call last): 295s File "/tmp/tmp.IMEgmk7sLf/test/subread-align/readname_ora_match.py", line 83, in 295s main() 295s ~~~~^^ 295s File "/tmp/tmp.IMEgmk7sLf/test/subread-align/readname_ora_match.py", line 80, in main 295s print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN)) 295s ~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~ 295s ZeroDivisionError: float division by zero 295s ************************************************* 295s *** SINGLE-END READS NO ERROR ****** 295s ************************************************* 295s 295s unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0 295s ************************************************* 295s *** SINGLE-END READS NO ERROR NO DUP ****** 295s ************************************************* 295s 295s unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0 295s 295s ************************************************* 295s *** READS WITH NO ERROR ****** 295s ************************************************* 295s 295s unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0 295s 295s ************************************************* 295s *** READS NO ERROR, NO DUPLICATED REPORT ****** 295s ************************************************* 295s 295s unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0 295s 295s ************************************************* 295s *** READS WITH ONLY SEQUENCING ERROR ****** 295s ************************************************* 295s 295s unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0 295s 295s ************************************************* 295s *** READS WITH SEQUENCING ERROR AND MUTATION *** 295s *** SUBREAD IS RUN WITH LONG INDEL DETECTION *** 295s ************************************************* 295s 295s unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0 295s 295s ========== _____ _ _ ____ _____ ______ _____ 295s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 295s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 295s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 295s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 295s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 295s v2.0.7 295s 295s //================================= setting ==================================\\ 295s || || 295s || Index name : small1 || 295s || Index space : base space || 295s || Memory : 3000 Mbytes || 295s || Repeat threshold : 100 repeats || 295s || Gapped index : yes || 295s || || 295s || Free / total memory : 0.2GB / 0.0GB || 295s || || 295s || Input files : 1 file in total || 295s || o chr901.fa || 295s || || 295s || || 295s || WARNING: the free memory is lower than 3.0GB. || 295s || the program may run very slow or crash. || 295s || || 295s \\============================================================================// 295s 295s //================================= Running ==================================\\ 295s || || 295s || Check the integrity of provided reference sequences ... || 295s || There were 4 notes for reference sequences. || 295s || The notes can be found in the log file, '../small1.log'. || 295s || Scan uninformative subreads in reference sequences ... || 296s subread-buildindex: hashtable.c:470: HashTablePutReplaceEx: Assertion `key != NULL' failed. 297s Aborted (core dumped) 297s 297s ========== _____ _ _ ____ _____ ______ _____ 297s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 297s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 297s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 297s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 297s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 297s v2.0.7 297s 297s //================================= setting ==================================\\ 297s || || 297s || Function : Read alignment + Junction detection (RNA-Seq) || 297s || Input file 1 : junction-reads-A.fq || 297s || Input file 2 : junction-reads-B.fq || 297s || Output file : junctions.sam (SAM) || 297s || Index name : small1 || 297s || || 297s || ------------------------------------ || 297s || || 297s || Threads : 1 || 297s || Phred offset : 33 || 297s || # of extracted subreads : 14 || 297s || Min read1 vote : 1 || 297s || Min read2 vote : 1 || 297s || Max fragment size : 600 || 297s || Min fragment size : 50 || 297s || Max mismatches : 3 || 297s || Max indel length : 5 || 297s || Report multi-mapping reads : no || 297s || Max alignments per multi-mapping read : 1 || 297s || || 297s \\============================================================================// 297s 297s //================= Running (15-Mar-2025 17:58:05, pid=1008) =================\\ 297s || || 297s || Check the input reads. || 297s || The input file contains base space reads. || 297s || Initialise the memory objects. || 297s || Estimate the mean read length. || 297s || The range of Phred scores observed in the data is [2,41] || 297s || Create the output SAM file. || 297s || Check the index. || 297s Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix. 297s 297s 297s ========== _____ _ _ ____ _____ ______ _____ 297s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 297s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 297s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 297s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 297s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 297s v2.0.7 297s 297s //================================= setting ==================================\\ 297s || || 297s || Function : Read alignment + Junction/Fusion detection (RNA-Seq) || 297s || Input file 1 : junction-reads-A.fq || 297s || Input file 2 : junction-reads-B.fq || 297s || Output file : junctionsNfusions.bam (BAM) || 297s || Index name : small1 || 297s || || 297s || ------------------------------------ || 297s || || 297s || Threads : 1 || 297s || Phred offset : 33 || 297s || # of extracted subreads : 28 || 297s || Min read1 vote : 1 || 297s || Min read2 vote : 1 || 297s || Max fragment size : 600 || 297s || Min fragment size : 50 || 297s || Max mismatches : 3 || 297s || Max indel length : 5 || 297s || Report multi-mapping reads : no || 297s || Max alignments per multi-mapping read : 1 || 297s || || 297s \\============================================================================// 297s 297s //================= Running (15-Mar-2025 17:58:05, pid=1009) =================\\ 297s || || 297s || Check the input reads. || 297s || The input file contains base space reads. || 297s || Initialise the memory objects. || 297s || Estimate the mean read length. || 297s 297s ================================================================================ 297s FeatureCounts Basic Test 297s http://subread.sourceforge.net/ 297s ================================================================================ 297s 297s ================================================================================ 297s Basic Test finished. 297s The results are in result/test-minimum.FC 297s ================================================================================ 297s 297s 297s 297s 297s ================================================================================ 297s FeatureCounts Chromosome Name Aliases Tests 297s http://subread.sourceforge.net/ 297s ================================================================================ 297s 297s || The range of Phred scores observed in the data is [2,41] || 297s || Create the output BAM file. || 297s || Check the index. || 297s Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix. 297s 297s 297s ========== _____ _ _ ____ _____ ______ _____ 297s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 297s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 297s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 297s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 297s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 297s v2.0.7 297s 297s Testing chromosome aliases ... [//========================== featureCounts setting ===========================\\ 297s || || 297s || Input files : 1 SAM file || 297s || || 297s || test-minimum.sam || 297s || || 297s || Output file : test-minimum.FC || 297s || Summary : test-minimum.FC.summary || 297s || Paired-end : yes || 297s || Count read pairs : no || 297s || Annotation : test-minimum.GTF (GTF) || 297s || Dir for temp files : result || 297s || || 297s || Threads : 1 || 297s || Level : meta-feature level || 297s || Multimapping reads : not counted || 297s || Multi-overlapping reads : not counted || 297s || Min overlapping bases : 1 || 297s || || 297s \\============================================================================// 297s 297s //================================= Running ==================================\\ 297s || || 297s || Load annotation file test-minimum.GTF ... || 297s || Features : 23 || 297s || Meta-features : 7 || 297s || Chromosomes/contigs : 3 || 297s || || 297s || Process SAM file test-minimum.sam... || 297s || Paired-end reads are included. || 297s || The reads are assigned on the single-end mode. || 297s || Total alignments : 998 || 297s || Successfully assigned alignments : 389 (39.0%) || 297s || Running time : 286331153.07 minutes || 297s || || 297s || Write the final count table. || 297s || Write the read assignment summary. || 297s || || 297s || Summary of counting results can be found in file "result/test-minimum.FC. || 297s || summary" || 297s || || 297s \\============================================================================// 297s 297s PASS] 297s 297s 297s ================================================================================ 297s FeatureCounts Chromosome Name Inference Tests 297s http://subread.sourceforge.net/ 297s ================================================================================ 297s 297s Testing automatic inference of chromosome names ... [PASS] 297s 297s mkdir: unrecognized option '--countReadPairs' 297s Try 'mkdir --help' for more information. 297s 297s ================================================================================ 297s FeatureCounts Corner Case Tests 297s http://subread.sourceforge.net/ 297s ================================================================================ 297s 297s Testing indel reads ... [PASS] 297s Testing junction reads ... [PASS] 297s Testing paired-end reads (fragment counting) ... [PASS] 297s Testing paired-end reads (fragment counting, both ends mapped) ... [PASS] 297s Testing multi-overlapping reads ... [PASS] 297s Testing feature-level summarization ... [PASS] 297s Testing gene-level summarization ... [PASS] 297s Testing multi-mapping reads ... [PASS] 297s Testing multi-mapping reads (primary only) ... [PASS] 297s Testing both ends mapped ... [PASS] 297s Testing disallowing chimeric fragments ... [PASS] 297s Testing Allowing multi-mapped reads ... [PASS] 297s Testing not sorting input file ... [PASS] 297s Testing minimum overlapping length ... [PASS] 297s Testing minimum overlapping fraction ... [PASS] 297s Testing Largest Overlapping ... [PASS] 297s Testing paired-end distance ... [PASS] 297s Testing Read to position (5' end) ... [PASS] 297s Testing Read to position (3' end) ... [PASS] 297s Testing Read extension to the 3' end ... [PASS] 297s Testing Read extension to the 5' end ... [PASS] 297s Testing Low maxOPs value ... [PASS] 297s Testing minimum mapping quality ... [PASS] 298s Testing Ignoring duplicated reads ... [PASS] 298s Testing Fraction counting ... [PASS] 298s Testing Advanced fractions ... [PASS] 298s Testing Junction counting ... [PASS,PASS] 298s Skipping Junction counting (with genome). 298s Testing GTF format annotations ... [PASS] 298s Testing SAF format annotations ... [PASS] 298s Testing SAM format input ... [PASS] 298s Testing BAM format input ... [PASS] 298s Testing unstranded read summarization ... [PASS] 298s Testing stranded read summarization ... [PASS] 298s Testing reversely stranded read summarization ... [PASS] 298s Testing Ignoring duplicate fragments ... [PASS] 298s Testing Junction reads only ... [PASS] 298s Testing Exonic reads only ... [PASS] 298s 298s Testing intron_between ... [PASS] 298s Testing intron_between ... [PASS] 298s Testing intron_between ... [PASS] 298s Testing intron_between ... [PASS] 298s Testing across_genes ... [PASS] 298s Testing across_genes ... [PASS] 298s Testing across_genes ... [PASS] 298s Testing across_genes ... [PASS] 298s Testing across_intron ... [PASS] 298s Testing across_intron ... [PASS] 298s Testing across_intron ... [PASS] 298s Testing across_intron ... [PASS] 298s ../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b 298s Check the input format ... 300s 300s ========== _____ _ _ ____ _____ ______ _____ 300s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 300s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 300s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 300s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 300s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 300s v2.0.7 300s 300s //============================= exactSNP setting =============================\\ 300s || || 300s || Input file : test-in.BAM (BAM) || 300s || Output file : test-out.VCF || 300s || Reference genome : chr901.fa || 300s || Temp path : || 300s || || 300s || Threads : 1 || 300s || Min supporting reads : 1 || 300s || Min pct. of supporting reads : 0.0% || 300s || Min base quality score : 13 || 300s || Number of trimmed bases : 3 || 300s || || 300s || Q value cutoff : 10E-12.0 || 300s || P value upper bound : 0.00500 || 300s || Flanking windows size : 5 || 300s || || 300s \\============================================================================// 300s 300s //====================== Running (15-Mar-2025 17:58:08) ======================\\ 300s || || 300s || Split BAM file into result/temp-snps-001600-00163EB95044-* ... || 302s || processed block chr901@999950 by thread 1/1 [block number=1/1] || 302s || || 302s || Completed successfully. || 302s || || 302s \\============================================================================// 302s 302s //================================= Summary ==================================\\ 302s || || 302s || Processed reads : 50204 || 302s || Reported SNPs : 416 || 302s || Reported indels : 22 || 302s || || 302s || Running time : -9091014109.8 minutes || 302s || || 302s \\============================================================================// 302s 302s  302s 302s ************************************************** 302s ************************************************** 302s *** *** 302s *** Test finished. *** 302s *** *** 302s *** Should there be any error, please visit *** 302s *** http://subread.sourceforge.net/ for more *** 302s *** information. *** 302s *** *** 302s ************************************************** 302s ************************************************** 302s 302s  302s 303s autopkgtest [17:58:11]: test subread-tests: -----------------------] 306s subread-tests PASS 306s autopkgtest [17:58:14]: test subread-tests: - - - - - - - - - - results - - - - - - - - - - 310s autopkgtest [17:58:18]: @@@@@@@@@@@@@@@@@@@@ summary 310s subread-tests PASS