0s autopkgtest [16:58:55]: starting date and time: 2025-03-15 16:58:55+0000 0s autopkgtest [16:58:55]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:58:55]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b7nh3mvn/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-29.secgroup --name adt-plucky-arm64-subread-20250315-165855-juju-7f2275-prod-proposed-migration-environment-2-3b08332a-cb95-4c01-a8d7-7c7d3c231577 --image adt/ubuntu-plucky-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,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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 179s autopkgtest [17:01:54]: testbed dpkg architecture: arm64 179s autopkgtest [17:01:54]: testbed apt version: 2.9.33 180s autopkgtest [17:01:55]: @@@@@@@@@@@@@@@@@@@@ test bed setup 180s autopkgtest [17:01:55]: testbed release detected to be: None 181s autopkgtest [17:01:56]: updating testbed package index (apt update) 181s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 181s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 182s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 182s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 182s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 182s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 182s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 182s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 182s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 182s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 182s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 183s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 183s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 183s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 183s Fetched 1078 kB in 2s (682 kB/s) 184s Reading package lists... 184s Reading package lists... 185s Building dependency tree... 185s Reading state information... 185s Calculating upgrade... 185s Calculating upgrade... 186s The following packages will be upgraded: 186s pinentry-curses python3-jinja2 strace 186s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 186s Need to get 647 kB of archives. 186s After this operation, 11.3 kB of additional disk space will be used. 186s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 187s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 187s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 188s Fetched 647 kB in 1s (586 kB/s) 188s (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 ... 117701 files and directories currently installed.) 188s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 188s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 188s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 188s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 188s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 188s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 188s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 188s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 188s Setting up strace (6.13+ds-1ubuntu1) ... 188s Processing triggers for man-db (2.13.0-1) ... 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 190s Solving dependencies... 190s The following packages will be REMOVED: 190s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 190s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 190s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 190s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 191s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 191s After this operation, 267 MB disk space will be freed. 191s (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 ... 117701 files and directories currently installed.) 191s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 191s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 191s Removing libpython3.12t64:arm64 (3.12.9-1) ... 191s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 191s Removing libnsl2:arm64 (1.3.0-3build3) ... 191s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 191s Removing libunwind8:arm64 (1.6.2-3.1) ... 191s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 191s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 193s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 193s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 193s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 193s /etc/kernel/postrm.d/initramfs-tools: 193s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 193s /etc/kernel/postrm.d/zz-flash-kernel: 193s flash-kernel: Kernel 6.11.0-8-generic has been removed. 193s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 194s /etc/kernel/postrm.d/zz-update-grub: 194s Sourcing file `/etc/default/grub' 194s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 194s Generating grub configuration file ... 194s Found linux image: /boot/vmlinuz-6.14.0-10-generic 194s Found initrd image: /boot/initrd.img-6.14.0-10-generic 194s Warning: os-prober will not be executed to detect other bootable partitions. 194s Systems on them will not be added to the GRUB boot configuration. 194s Check GRUB_DISABLE_OS_PROBER documentation entry. 194s Adding boot menu entry for UEFI Firmware Settings ... 194s done 194s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 195s Processing triggers for libc-bin (2.41-1ubuntu1) ... 195s (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 ... 81650 files and directories currently installed.) 195s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 195s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 195s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 195s autopkgtest [17:02:10]: upgrading testbed (apt dist-upgrade and autopurge) 195s Reading package lists... 196s Building dependency tree... 196s Reading state information... 196s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 196s Starting 2 pkgProblemResolver with broken count: 0 196s Done 197s Entering ResolveByKeep 197s 198s Calculating upgrade... 198s The following packages will be upgraded: 198s libc-bin libc-dev-bin libc6 libc6-dev locales 198s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s Need to get 9530 kB of archives. 198s After this operation, 0 B of additional disk space will be used. 198s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 200s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 200s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 203s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 204s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 209s Preconfiguring packages ... 209s Fetched 9530 kB in 10s (913 kB/s) 209s (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 ... 81647 files and directories currently installed.) 209s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 209s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 209s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 209s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 209s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 209s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 210s Setting up libc6:arm64 (2.41-1ubuntu2) ... 210s (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 ... 81647 files and directories currently installed.) 210s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 210s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 210s Setting up libc-bin (2.41-1ubuntu2) ... 210s (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 ... 81647 files and directories currently installed.) 210s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 210s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 210s Setting up locales (2.41-1ubuntu2) ... 211s Generating locales (this might take a while)... 213s en_US.UTF-8... done 213s Generation complete. 213s Setting up libc-dev-bin (2.41-1ubuntu2) ... 213s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 213s Processing triggers for man-db (2.13.0-1) ... 214s Processing triggers for systemd (257.3-1ubuntu3) ... 215s Reading package lists... 215s Building dependency tree... 215s Reading state information... 216s Starting pkgProblemResolver with broken count: 0 216s Starting 2 pkgProblemResolver with broken count: 0 216s Done 216s Solving dependencies... 217s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 217s autopkgtest [17:02:32]: rebooting testbed after setup commands that affected boot 240s autopkgtest [17:02:55]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 243s autopkgtest [17:02:58]: @@@@@@@@@@@@@@@@@@@@ apt-source subread 264s Get:1 http://ftpmaster.internal/ubuntu plucky/universe subread 2.0.7+dfsg-1 (dsc) [2332 B] 264s Get:2 http://ftpmaster.internal/ubuntu plucky/universe subread 2.0.7+dfsg-1 (tar) [16.5 MB] 264s Get:3 http://ftpmaster.internal/ubuntu plucky/universe subread 2.0.7+dfsg-1 (diff) [19.6 kB] 264s gpgv: Signature made Sat Aug 31 10:04:54 2024 UTC 264s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 264s gpgv: issuer "emollier@debian.org" 264s gpgv: Can't check signature: No public key 264s dpkg-source: warning: cannot verify inline signature for ./subread_2.0.7+dfsg-1.dsc: no acceptable signature found 265s autopkgtest [17:03:20]: testing package subread version 2.0.7+dfsg-1 265s autopkgtest [17:03:20]: build not needed 269s autopkgtest [17:03:24]: test subread-tests: preparing testbed 269s Reading package lists... 269s Building dependency tree... 269s Reading state information... 270s Starting pkgProblemResolver with broken count: 0 270s Starting 2 pkgProblemResolver with broken count: 0 270s Done 270s The following NEW packages will be installed: 270s subread subread-data 271s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 271s Need to get 19.8 MB of archives. 271s After this operation, 21.5 MB of additional disk space will be used. 271s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 subread arm64 2.0.7+dfsg-1 [549 kB] 271s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 subread-data all 2.0.7+dfsg-1 [19.2 MB] 293s Fetched 19.8 MB in 22s (909 kB/s) 293s Selecting previously unselected package subread. 293s (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 ... 81647 files and directories currently installed.) 293s Preparing to unpack .../subread_2.0.7+dfsg-1_arm64.deb ... 293s Unpacking subread (2.0.7+dfsg-1) ... 293s Selecting previously unselected package subread-data. 293s Preparing to unpack .../subread-data_2.0.7+dfsg-1_all.deb ... 293s Unpacking subread-data (2.0.7+dfsg-1) ... 293s Setting up subread (2.0.7+dfsg-1) ... 293s Setting up subread-data (2.0.7+dfsg-1) ... 293s Processing triggers for man-db (2.13.0-1) ... 295s autopkgtest [17:03:50]: test subread-tests: [----------------------- 296s  296s 296s 296s 296s ************************************************** 296s ************************************************** 296s *** *** 296s *** This script will test the major functions *** 296s *** in our package, including the index build- *** 296s *** er, subread-align, subjunc, featureCounts *** 296s *** and exactSNP. *** 296s *** *** 296s *** Test will start in seconds. *** 296s *** *** 296s ************************************************** 296s ************************************************** 296s 297s 9test_all.sh: line 25: bc: command not found 298s test_all.sh: line 25: bc: command not found 299s test_all.sh: line 25: bc: command not found 300s test_all.sh: line 25: bc: command not found 301s test_all.sh: line 25: bc: command not found 302s test_all.sh: line 25: bc: command not found 303s test_all.sh: line 25: bc: command not found 304s test_all.sh: line 25: bc: command not found 305s test_all.sh: line 25: bc: command not found 305s [0,0Hrm: cannot remove 'test-tmp.log': No such file or directory 305s 305s ========== _____ _ _ ____ _____ ______ _____ 305s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 305s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 305s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 305s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 305s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 305s v2.0.7 305s 305s //================================= setting ==================================\\ 305s || || 305s || Index name : small1 || 305s || Index space : base space || 305s || Index split : no-split || 305s || Repeat threshold : 100 repeats || 305s || Gapped index : no || 305s || || 305s || Free / total memory : 3.6GB / 3.8GB || 305s || || 305s || Input files : 1 file in total || 305s || o chr901.fa || 305s || || 305s \\============================================================================// 305s 305s //================================= Running ==================================\\ 305s || || 305s || Check the integrity of provided reference sequences ... || 305s || There were 4 notes for reference sequences. || 305s || The notes can be found in the log file, '../small1.log'. || 305s || Scan uninformative subreads in reference sequences ... || 307s || 52 uninformative subreads were found. || 307s || These subreads were excluded from index building. || 307s || Estimate the index size... || 307s || 8%, 0 mins elapsed, rate=570.3k bps/s || 307s || 16%, 0 mins elapsed, rate=1035.0k bps/s || 307s || 25%, 0 mins elapsed, rate=1429.0k bps/s || 307s || 33%, 0 mins elapsed, rate=1764.9k bps/s || 307s || 41%, 0 mins elapsed, rate=2054.7k bps/s || 307s || 50%, 0 mins elapsed, rate=2296.8k bps/s || 307s || 58%, 0 mins elapsed, rate=2507.8k bps/s || 307s || 66%, 0 mins elapsed, rate=2693.4k bps/s || 307s || 75%, 0 mins elapsed, rate=2868.8k bps/s || 307s || 83%, 0 mins elapsed, rate=3026.4k bps/s || 307s || 91%, 0 mins elapsed, rate=3168.9k bps/s || 307s || 3.0 GB of memory is needed for index building. || 308s || Build the index... || 309s || 8%, 0 mins elapsed, rate=49.4k bps/s || 309s || 16%, 0 mins elapsed, rate=97.3k bps/s || 309s || 25%, 0 mins elapsed, rate=143.9k bps/s || 309s || 33%, 0 mins elapsed, rate=189.1k bps/s || 309s || 41%, 0 mins elapsed, rate=233.1k bps/s || 309s || 50%, 0 mins elapsed, rate=275.8k bps/s || 309s || 58%, 0 mins elapsed, rate=317.2k bps/s || 309s || 66%, 0 mins elapsed, rate=357.5k bps/s || 309s || 75%, 0 mins elapsed, rate=396.7k bps/s || 309s || 83%, 0 mins elapsed, rate=435.0k bps/s || 309s || 91%, 0 mins elapsed, rate=472.2k bps/s || 309s || Save current index block... || 309s || [ 0.0% finished ] || 310s || [ 10.0% finished ] || 310s || [ 20.0% finished ] || 311s || [ 30.0% finished ] || 311s || [ 40.0% finished ] || 311s || [ 50.0% finished ] || 312s || [ 60.0% finished ] || 312s || [ 70.0% finished ] || 313s || [ 80.0% finished ] || 313s || [ 90.0% finished ] || 313s || [ 100.0% finished ] || 313s || || 314s || Total running time: 0.1 minutes. || 314s || Index ../small1 was successfully built. || 314s || || 314s \\============================================================================// 314s 315s 315s ========== _____ _ _ ____ _____ ______ _____ 315s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 315s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 315s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 315s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 315s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 315s v2.0.7 315s 315s //================================= setting ==================================\\ 315s || || 315s || Function : Read alignment (RNA-Seq) || 315s || Input file : test-noerror-r1.fq || 315s || Output file : test-tmp.sam (SAM) || 315s || Index name : small1 || 315s || || 315s || ------------------------------------ || 315s || || 315s || Threads : 1 || 315s || Phred offset : 64 || 315s || Min votes : 3 / 10 || 315s || Max mismatches : 3 || 315s || Max indel length : 5 || 315s || Report multi-mapping reads : no || 315s || Max alignments per multi-mapping read : 1 || 315s || || 315s \\============================================================================// 315s 315s //================= Running (15-Mar-2025 17:04:10, pid=1468) =================\\ 315s || || 315s || Check the input reads. || 315s || The input file contains base space reads. || 315s || Initialise the memory objects. || 315s || Estimate the mean read length. || 315s || The range of Phred scores observed in the data is [9,9] || 315s || Create the output SAM file. || 315s || Check the index. || 315s || Init the voting space. || 315s || Global environment is initialised. || 315s || Load the 1-th index block... || 341s || The index block has been loaded. || 341s || Start read mapping in chunk. || 342s || 33% completed, 0.4 mins elapsed, rate=56.0k reads per second || 342s || 74% completed, 0.4 mins elapsed, rate=0.6k reads per second || 342s || 83% completed, 0.4 mins elapsed, rate=0.6k reads per second || 342s || 91% completed, 0.4 mins elapsed, rate=0.7k reads per second || 342s || || 342s || Completed successfully. || 342s || || 342s \\==================================== ====================================// 342s 342s //================================ Summary =================================\\ 342s || || 342s || Total reads : 19998 || 342s || Mapped : 18785 (93.9%) || 342s || Uniquely mapped : 18785 || 342s || Multi-mapping : 0 || 342s || || 342s || Unmapped : 1213 || 342s || || 342s || Indels : 0 || 342s || || 342s || Running time : 0.5 minutes || 342s || || 342s \\============================================================================// 342s 342s 342s ========== _____ _ _ ____ _____ ______ _____ 342s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 342s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 342s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 342s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 342s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 342s v2.0.7 342s 342s //================================= setting ==================================\\ 342s || || 342s || Function : Read alignment (RNA-Seq) || 342s || Input file : test-noerror-r1.fq || 342s || Output file : test-tmp.sam (SAM) || 342s || Index name : small1 || 342s || || 342s || ------------------------------------ || 342s || || 342s || Threads : 1 || 342s || Phred offset : 64 || 342s || Min votes : 3 / 10 || 342s || Max mismatches : 3 || 342s || Max indel length : 5 || 342s || Report multi-mapping reads : no || 342s || Max alignments per multi-mapping read : 1 || 342s || || 342s \\============================================================================// 342s 342s //================= Running (15-Mar-2025 17:04:37, pid=1472) =================\\ 342s || || 342s || Check the input reads. || 342s || The input file contains base space reads. || 342s || Initialise the memory objects. || 342s || Estimate the mean read length. || 342s || The range of Phred scores observed in the data is [9,9] || 342s || Create the output SAM file. || 342s || Check the index. || 342s || Init the voting space. || 342s || Global environment is initialised. || 342s || Load the 1-th index block... || 368s || The index block has been loaded. || 368s || Start read mapping in chunk. || 368s || 33% completed, 0.4 mins elapsed, rate=58.0k reads per second || 369s || 74% completed, 0.4 mins elapsed, rate=0.6k reads per second || 369s || 83% completed, 0.4 mins elapsed, rate=0.6k reads per second || 369s || 91% completed, 0.4 mins elapsed, rate=0.7k reads per second || 369s || || 369s || Completed successfully. || 369s || || 369s \\==================================== ====================================// 369s 369s //================================ Summary =================================\\ 369s || || 369s || Total reads : 19998 || 369s || Mapped : 18785 (93.9%) || 369s || Uniquely mapped : 18785 || 369s || Multi-mapping : 0 || 369s || || 369s || Unmapped : 1213 || 369s || || 369s || Indels : 0 || 369s || || 369s || Running time : 0.4 minutes || 369s || || 369s \\============================================================================// 369s 369s 369s ========== _____ _ _ ____ _____ ______ _____ 369s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 369s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 369s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 369s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 369s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 369s v2.0.7 369s 369s //================================= setting ==================================\\ 369s || || 369s || Function : Read alignment (RNA-Seq) || 369s || Input file 1 : test-noerror-r1.fq || 369s || Input file 2 : test-noerror-r2.fq || 369s || Output file : test-tmp.sam (SAM) || 369s || Index name : small1 || 369s || || 369s || ------------------------------------ || 369s || || 369s || Threads : 1 || 369s || Phred offset : 64 || 369s || # of extracted subreads : 10 || 369s || Min read1 vote : 3 || 369s || Min read2 vote : 1 || 369s || Max fragment size : 600 || 369s || Min fragment size : 50 || 369s || Max mismatches : 3 || 369s || Max indel length : 5 || 369s || Report multi-mapping reads : no || 369s || Max alignments per multi-mapping read : 1 || 369s || || 369s \\============================================================================// 369s 369s //================= Running (15-Mar-2025 17:05:04, pid=1479) =================\\ 369s || || 369s || Check the input reads. || 369s || The input file contains base space reads. || 369s || Initialise the memory objects. || 369s || Estimate the mean read length. || 369s || The range of Phred scores observed in the data is [9,9] || 369s || Create the output SAM file. || 369s || Check the index. || 369s || Init the voting space. || 369s || Global environment is initialised. || 369s || Load the 1-th index block... || 395s || The index block has been loaded. || 395s || Start read mapping in chunk. || 396s || 33% completed, 0.4 mins elapsed, rate=27.9k fragments per second || 396s || Estimated fragment length : 495 bp || 396s || 74% completed, 0.5 mins elapsed, rate=0.5k fragments per second || 396s || 83% completed, 0.5 mins elapsed, rate=0.6k fragments per second || 396s || 91% completed, 0.5 mins elapsed, rate=0.7k fragments per second || 397s || || 397s || Completed successfully. || 397s || || 397s \\==================================== ====================================// 397s 397s //================================ Summary =================================\\ 397s || || 397s || Total fragments : 19998 || 397s || Mapped : 19491 (97.5%) || 397s || Uniquely mapped : 19491 || 397s || Multi-mapping : 0 || 397s || || 397s || Unmapped : 507 || 397s || || 397s || Properly paired : 19089 || 397s || Not properly paired : 402 || 397s || Singleton : 0 || 397s || Chimeric : 0 || 397s || Unexpected strandness : 0 || 397s || Unexpected fragment length : 385 || 397s || Unexpected read order : 17 || 397s || || 397s || Indels : 0 || 397s || || 397s || Running time : 0.5 minutes || 397s || || 397s \\============================================================================// 397s 397s 397s ========== _____ _ _ ____ _____ ______ _____ 397s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 397s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 397s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 397s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 397s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 397s v2.0.7 397s 397s //================================= setting ==================================\\ 397s || || 397s || Function : Read alignment (RNA-Seq) || 397s || Input file 1 : test-noerror-r1.fq || 397s || Input file 2 : test-noerror-r2.fq || 397s || Output file : test-tmp.sam (SAM) || 397s || Index name : small1 || 397s || || 397s || ------------------------------------ || 397s || || 397s || Threads : 1 || 397s || Phred offset : 64 || 397s || # of extracted subreads : 10 || 397s || Min read1 vote : 3 || 397s || Min read2 vote : 1 || 397s || Max fragment size : 600 || 397s || Min fragment size : 50 || 397s || Max mismatches : 3 || 397s || Max indel length : 5 || 397s || Report multi-mapping reads : no || 397s || Max alignments per multi-mapping read : 1 || 397s || || 397s \\============================================================================// 397s 397s //================= Running (15-Mar-2025 17:05:32, pid=1483) =================\\ 397s || || 397s || Check the input reads. || 397s || The input file contains base space reads. || 397s || Initialise the memory objects. || 397s || Estimate the mean read length. || 397s || The range of Phred scores observed in the data is [9,9] || 397s || Create the output SAM file. || 397s || Check the index. || 397s || Init the voting space. || 397s || Global environment is initialised. || 397s || Load the 1-th index block... || 423s || The index block has been loaded. || 423s || Start read mapping in chunk. || 423s || 33% completed, 0.4 mins elapsed, rate=26.6k fragments per second || 424s || Estimated fragment length : 495 bp || 424s || 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || 424s || 83% completed, 0.5 mins elapsed, rate=0.6k fragments per second || 424s || 91% completed, 0.5 mins elapsed, rate=0.7k fragments per second || 424s || || 424s || Completed successfully. || 424s || || 424s \\==================================== ====================================// 424s 424s //================================ Summary =================================\\ 424s || || 424s || Total fragments : 19998 || 424s || Mapped : 19491 (97.5%) || 424s || Uniquely mapped : 19491 || 424s || Multi-mapping : 0 || 424s || || 424s || Unmapped : 507 || 424s || || 424s || Properly paired : 19089 || 424s || Not properly paired : 402 || 424s || Singleton : 0 || 424s || Chimeric : 0 || 424s || Unexpected strandness : 0 || 424s || Unexpected fragment length : 385 || 424s || Unexpected read order : 17 || 424s || || 424s || Indels : 0 || 424s || || 424s || Running time : 0.5 minutes || 424s || || 424s \\============================================================================// 424s 424s 424s ========== _____ _ _ ____ _____ ______ _____ 424s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 424s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 424s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 424s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 424s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 424s v2.0.7 424s 424s //================================= setting ==================================\\ 424s || || 424s || Function : Read alignment (RNA-Seq) || 424s || Input file 1 : test-error-r1.fq || 424s || Input file 2 : test-error-r2.fq || 424s || Output file : test-tmp.sam (SAM) || 424s || Index name : small1 || 424s || || 424s || ------------------------------------ || 424s || || 424s || Threads : 1 || 424s || Phred offset : 64 || 424s || # of extracted subreads : 10 || 424s || Min read1 vote : 3 || 424s || Min read2 vote : 1 || 424s || Max fragment size : 600 || 424s || Min fragment size : 50 || 424s || Max mismatches : 3 || 424s || Max indel length : 5 || 424s || Report multi-mapping reads : no || 424s || Max alignments per multi-mapping read : 1 || 424s || || 424s \\============================================================================// 424s 424s //================= Running (15-Mar-2025 17:05:59, pid=1487) =================\\ 424s || || 424s || Check the input reads. || 424s || The input file contains base space reads. || 424s || Initialise the memory objects. || 424s || Estimate the mean read length. || 424s || The range of Phred scores observed in the data is [-14,-14] || 424s || Create the output SAM file. || 424s || Check the index. || 424s || Init the voting space. || 424s || Global environment is initialised. || 424s || Load the 1-th index block... || 450s || The index block has been loaded. || 450s || Start read mapping in chunk. || 451s || 33% completed, 0.4 mins elapsed, rate=30.6k fragments per second || 451s || Estimated fragment length : 497 bp || 451s || 74% completed, 0.5 mins elapsed, rate=0.6k fragments per second || 451s || 83% completed, 0.5 mins elapsed, rate=0.6k fragments per second || 451s || 91% completed, 0.5 mins elapsed, rate=0.7k fragments per second || 451s || || 451s || Completed successfully. || 451s || || 451s \\==================================== ====================================// 451s 451s //================================ Summary =================================\\ 451s || || 451s || Total fragments : 20000 || 451s || Mapped : 18937 (94.7%) || 451s || Uniquely mapped : 18937 || 451s || Multi-mapping : 0 || 451s || || 451s || Unmapped : 1063 || 451s || || 451s || Properly paired : 14143 || 451s || Not properly paired : 4794 || 451s || Singleton : 4504 || 451s || Chimeric : 0 || 451s || Unexpected strandness : 0 || 451s || Unexpected fragment length : 274 || 451s || Unexpected read order : 16 || 451s || || 451s || Indels : 15 || 451s || || 451s || Running time : 0.5 minutes || 451s || || 451s \\============================================================================// 451s 452s 452s ========== _____ _ _ ____ _____ ______ _____ 452s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 452s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 452s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 452s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 452s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 452s v2.0.7 452s 452s //================================= setting ==================================\\ 452s || || 452s || Function : Read alignment (RNA-Seq) || 452s || Input file 1 : test-err-mut-r1.fq.gz || 452s || Input file 2 : test-err-mut-r2.fq.gz || 452s || Output file : test-tmp.sam (SAM) || 452s || Index name : small1 || 452s || || 452s || ------------------------------------ || 452s || || 452s || Threads : 1 || 452s || Phred offset : 64 || 452s || # of extracted subreads : 10 || 452s || Min read1 vote : 3 || 452s || Min read2 vote : 1 || 452s || Max fragment size : 600 || 452s || Min fragment size : 50 || 452s || Max mismatches : 3 || 452s || Max indel length : 5 || 452s || Report multi-mapping reads : no || 452s || Max alignments per multi-mapping read : 1 || 452s || Read group name : MyTestGroup || 452s || || 452s \\============================================================================// 452s 452s //================= Running (15-Mar-2025 17:06:27, pid=1491) =================\\ 452s || || 452s 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. 452s 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. 452s 76f6c2a84c5097b13435bbeac4a8acd8 ../small1.00.b.array 452s 39cd407b95c866d7db864ce69a7d08fb ../small1.00.b.tab 452s ************************************************* 452s *** SINGLE-END READS NO ERROR ****** 452s ************************************************* 452s 452s unmatched= 0 ; matched= 18785 ; unmapped= 1213 ; reads= 19998 ;NN= 0 452s accuracy= 1.0 ; sensitivity= 0.9393439343934393 452s paired_match= 0 ; paired= 0.0 452s ************************************************* 452s *** SINGLE-END READS NO ERROR NO DUP ****** 452s ************************************************* 452s 452s unmatched= 0 ; matched= 18785 ; unmapped= 1213 ; reads= 19998 ;NN= 0 452s accuracy= 1.0 ; sensitivity= 0.9393439343934393 452s paired_match= 0 ; paired= 0.0 452s 452s ************************************************* 452s *** READS WITH NO ERROR ****** 452s ************************************************* 452s 452s unmatched= 56 ; matched= 38926 ; unmapped= 1014 ; reads= 39996 ;NN= 0 452s accuracy= 0.9985634395361962 ; sensitivity= 0.9746474647464747 452s paired_match= 38926 ; paired= 1.0 452s 452s ************************************************* 452s *** READS NO ERROR, NO DUPLICATED REPORT ****** 452s ************************************************* 452s 452s unmatched= 56 ; matched= 38926 ; unmapped= 1014 ; reads= 39996 ;NN= 0 452s accuracy= 0.9985634395361962 ; sensitivity= 0.9746474647464747 452s paired_match= 38926 ; paired= 1.0 452s 452s ************************************************* 452s *** READS WITH ONLY SEQUENCING ERROR ****** 452s ************************************************* 452s 452s unmatched= 66 ; matched= 33304 ; unmapped= 6630 ; reads= 40000 ;NN= 0 452s accuracy= 0.9980221756068325 ; sensitivity= 0.83425 452s paired_match= 28800 ; paired= 0.8647609896709104 452s 452s ************************************************* 452s *** READS WITH SEQUENCING ERROR AND MUTATION *** 452s *** SUBREAD IS RUN WITH LONG INDEL DETECTION *** 452s ************************************************* 452s 452s unmatched= 66 ; matched= 33304 ; unmapped= 6630 ; reads= 40000 ;NN= 0 452s accuracy= 0.9980221756068325 ; sensitivity= 0.83425 452s paired_match= 28800 ; paired= 0.8647609896709104 452s 452s ========== _____ _ _ ____ _____ ______ _____ 452s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 452s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 452s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 452s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 452s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 452s v2.0.7 452s 452s //================================= setting ==================================\\ 452s || || 452s || Index name : small1 || 452s || Index space : base space || 452s || Memory : 8000 Mbytes || 452s || Repeat threshold : 100 repeats || 452s || Gapped index : yes || 452s || || 452s || Free / total memory : 3.5GB / 3.8GB || 452s || || 452s || Input files : 1 file in total || 452s || o chr901.fa || 452s || || 452s \\============================================================================// 452s 452s //================================= Running ==================================\\ 452s || || 452s || Check the integrity of provided reference sequences ... || 452s || There were 4 notes for reference sequences. || 452s || The notes can be found in the log file, '../small1.log'. || 452s || Scan uninformative subreads in reference sequences ... || 453s || 2 uninformative subreads were found. || 453s || These subreads were excluded from index building. || 453s || Estimate the index size... || 453s || 8%, 0 mins elapsed, rate=4191.6k bps/s || 453s || 16%, 0 mins elapsed, rate=6706.5k bps/s || 453s || 25%, 0 mins elapsed, rate=8383.2k bps/s || 453s || 33%, 0 mins elapsed, rate=9580.8k bps/s || 453s || 41%, 0 mins elapsed, rate=10478.9k bps/s || 453s || 50%, 0 mins elapsed, rate=11177.6k bps/s || 453s || 58%, 0 mins elapsed, rate=11736.4k bps/s || 453s || 66%, 0 mins elapsed, rate=12193.7k bps/s || 453s || 75%, 0 mins elapsed, rate=12574.8k bps/s || 453s || 83%, 0 mins elapsed, rate=12897.2k bps/s || 453s || 91%, 0 mins elapsed, rate=13173.6k bps/s || 453s || 0.8 GB of memory is needed for index building. || 453s || Build the index... || 453s || 8%, 0 mins elapsed, rate=453.1k bps/s || 453s || 16%, 0 mins elapsed, rate=864.2k bps/s || 453s || 25%, 0 mins elapsed, rate=1245.0k bps/s || 453s || 33%, 0 mins elapsed, rate=1589.2k bps/s || 453s || 41%, 0 mins elapsed, rate=1914.0k bps/s || 453s || 50%, 0 mins elapsed, rate=2215.8k bps/s || 453s || 58%, 0 mins elapsed, rate=2486.5k bps/s || 453s || 66%, 0 mins elapsed, rate=2748.6k bps/s || 453s || 75%, 0 mins elapsed, rate=2994.0k bps/s || 453s || 83%, 0 mins elapsed, rate=3212.0k bps/s || 453s || 91%, 0 mins elapsed, rate=3428.1k bps/s || 453s || Save current index block... || 453s || [ 0.0% finished ] || 453s || [ 10.0% finished ] || 453s || [ 20.0% finished ] || 453s || [ 30.0% finished ] || 453s || [ 40.0% finished ] || 453s || [ 50.0% finished ] || 453s || [ 60.0% finished ] || 454s || [ 70.0% finished ] || 454s || [ 80.0% finished ] || 454s || [ 90.0% finished ] || 454s || [ 100.0% finished ] || 454s || || 454s || Total running time: 0.0 minutes. || 454s || Index ../small1 was successfully built. || 454s || || 454s \\============================================================================// 454s 454s 454s ========== _____ _ _ ____ _____ ______ _____ 454s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 454s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 454s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 454s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 454s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 454s v2.0.7 454s 454s //================================= setting ==================================\\ 454s || || 454s || Function : Read alignment + Junction detection (RNA-Seq) || 454s || Input file 1 : junction-reads-A.fq || 454s || Input file 2 : junction-reads-B.fq || 454s || Output file : junctions.sam (SAM) || 454s || Index name : small1 || 454s || || 454s || ------------------------------------ || 454s || || 454s || Threads : 1 || 454s || Phred offset : 33 || 454s || # of extracted subreads : 14 || 454s || Min read1 vote : 1 || 454s || Min read2 vote : 1 || 454s || Max fragment size : 600 || 454s || Min fragment size : 50 || 454s || Max mismatches : 3 || 454s || Max indel length : 5 || 454s || Report multi-mapping reads : no || 454s || Max alignments per multi-mapping read : 1 || 454s || || 454s \\============================================================================// 454s 454s //================= Running (15-Mar-2025 17:06:29, pid=1498) =================\\ 454s || || 454s || Check the input reads. || 454s || The input file contains base space reads. || 454s || Initialise the memory objects. || 454s || Estimate the mean read length. || 454s || The range of Phred scores observed in the data is [2,41] || 454s || Create the output SAM file. || 454s || Check the index. || 454s || Init the voting space. || 454s || Global environment is initialised. || 454s || Load the 1-th index block... || 457s || The index block has been loaded. || 457s || Start read mapping in chunk. || 458s || 41% completed, 0.1 mins elapsed, rate=15.5k fragments per second || 458s || Estimated fragment length : 173 bp || 458s || 77% completed, 0.1 mins elapsed, rate=2.9k fragments per second || 458s || 87% completed, 0.1 mins elapsed, rate=3.2k fragments per second || 458s || 97% completed, 0.1 mins elapsed, rate=3.5k fragments per second || 458s || || 458s || Completed successfully. || 458s || || 458s \\==================================== ====================================// 458s 458s //================================ Summary =================================\\ 458s || || 458s || Total fragments : 16052 || 458s || Mapped : 15291 (95.3%) || 458s || Uniquely mapped : 15291 || 458s || Multi-mapping : 0 || 458s || || 458s || Unmapped : 761 || 458s || || 458s || Properly paired : 13894 || 458s || Not properly paired : 1397 || 458s || Singleton : 962 || 458s || Chimeric : 0 || 458s || Unexpected strandness : 36 || 458s || Unexpected fragment length : 335 || 458s || Unexpected read order : 64 || 458s || || 458s || Junctions : 419 || 458s || Indels : 177 || 458s || || 458s || Running time : 0.1 minutes || 458s || || 458s \\============================================================================// 458s 458s 458s ========== _____ _ _ ____ _____ ______ _____ 458s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 458s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 458s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 458s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 458s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 458s v2.0.7 458s 458s //================================= setting ==================================\\ 458s || || 458s || Function : Read alignment + Junction/Fusion detection (RNA-Seq) || 458s || Input file 1 : junction-reads-A.fq || 458s || Input file 2 : junction-reads-B.fq || 458s || Output file : junctionsNfusions.bam (BAM) || 458s || Index name : small1 || 458s || || 458s || ------------------------------------ || 458s || || 458s || Threads : 1 || 458s || Phred offset : 33 || 458s || # of extracted subreads : 28 || 458s || Min read1 vote : 1 || 458s || Min read2 vote : 1 || 458s || Max fragment size : 600 || 458s || Min fragment size : 50 || 458s || Max mismatches : 3 || 458s || Max indel length : 5 || 458s || Report multi-mapping reads : no || 458s || Max alignments per multi-mapping read : 1 || 458s || || 458s \\============================================================================// 458s 458s //================= Running (15-Mar-2025 17:06:33, pid=1500) =================\\ 458s || || 458s || Check the input reads. || 458s || The input file contains base space reads. || 458s || Initialise the memory objects. || 458s || Estimate the mean read length. || 458s || The range of Phred scores observed in the data is [2,41] || 458s || Create the output BAM file. || 458s || Check the index. || 458s || Init the voting space. || 459s || Global environment is initialised. || 459s || Load the 1-th index block... || 462s || The index block has been loaded. || 462s || Start read mapping in chunk. || 463s || 41% completed, 0.1 mins elapsed, rate=8.5k fragments per second || 463s || Estimated fragment length : 174 bp || 463s || 77% completed, 0.1 mins elapsed, rate=2.5k fragments per second || 463s || 87% completed, 0.1 mins elapsed, rate=2.7k fragments per second || 464s || 97% completed, 0.1 mins elapsed, rate=3.0k fragments per second || 464s || || 464s || Completed successfully. || 464s || || 464s \\==================================== ====================================// 464s 464s //================================ Summary =================================\\ 464s || || 464s || Total fragments : 16052 || 464s || Mapped : 15273 (95.1%) || 464s || Uniquely mapped : 15273 || 464s || Multi-mapping : 0 || 464s || || 464s || Unmapped : 779 || 464s || || 464s || Properly paired : 13793 || 464s || Not properly paired : 1480 || 464s || Singleton : 1013 || 464s || Chimeric : 0 || 464s || Unexpected strandness : 37 || 464s || Unexpected fragment length : 368 || 464s || Unexpected read order : 62 || 464s || || 464s || Junctions : 437 || 464s || Fusions : 33 || 464s || Indels : 180 || 464s || || 464s || Running time : 0.1 minutes || 464s || || 464s \\============================================================================// 464s 464s 464s ================================================================================ 464s FeatureCounts Basic Test 464s http://subread.sourceforge.net/ 464s ================================================================================ 464s 464s 464s ========== _____ _ _ ____ _____ ______ _____ 464s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 464s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 464s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 464s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 464s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 464s v2.0.7 464s 464s //========================== featureCounts setting ===========================\\ 464s || || 464s || Input files : 1 SAM file || 464s || || 464s || test-minimum.sam || 464s || || 464s || Output file : test-minimum.FC || 464s || Summary : test-minimum.FC.summary || 464s || Paired-end : yes || 464s || Count read pairs : no || 464s || Annotation : test-minimum.GTF (GTF) || 464s || Dir for temp files : result || 464s || || 464s || Threads : 1 || 464s || Level : meta-feature level || 464s || Multimapping reads : not counted || 464s || Multi-overlapping reads : not counted || 464s || Min overlapping bases : 1 || 464s || || 464s \\============================================================================// 464s 464s //================================= Running ==================================\\ 464s || || 464s || Load annotation file test-minimum.GTF ... || 464s || Features : 23 || 464s || Meta-features : 7 || 464s || Chromosomes/contigs : 3 || 464s || || 464s || Process SAM file test-minimum.sam... || 464s ================================================================================ 464s Basic Test finished. 464s The results are in result/test-minimum.FC 464s ================================================================================ 464s 464s 464s 464s 464s ================================================================================ 464s FeatureCounts Chromosome Name Aliases Tests 464s http://subread.sourceforge.net/ 464s ================================================================================ 464s 464s Testing chromosome aliases ... [|| Paired-end reads are included. || 464s || The reads are assigned on the single-end mode. || 464s || Total alignments : 998 || 464s || Successfully assigned alignments : 389 (39.0%) || 464s || Running time : 0.00 minutes || 464s || || 464s || Write the final count table. || 464s || Write the read assignment summary. || 464s || || 464s || Summary of counting results can be found in file "result/test-minimum.FC. || 464s || summary" || 464s || || 464s \\============================================================================// 464s 464s PASS] 464s 464s 464s ================================================================================ 464s FeatureCounts Chromosome Name Inference Tests 464s http://subread.sourceforge.net/ 464s ================================================================================ 464s 464s Testing automatic inference of chromosome names ... [PASS] 464s 464s 464s ================================================================================ 464s FeatureCounts Corner Case Tests 464s http://subread.sourceforge.net/ 464s ================================================================================ 464s 464s mkdir: unrecognized option '--countReadPairs' 464s Try 'mkdir --help' for more information. 464s Testing indel reads ... [PASS] 464s Testing junction reads ... [PASS] 464s Testing paired-end reads (fragment counting) ... [PASS] 464s Testing paired-end reads (fragment counting, both ends mapped) ... [PASS] 464s Testing multi-overlapping reads ... [PASS] 464s Testing feature-level summarization ... [PASS] 464s Testing gene-level summarization ... [PASS] 464s Testing multi-mapping reads ... [PASS] 464s Testing multi-mapping reads (primary only) ... [PASS] 464s Testing both ends mapped ... [PASS] 464s Testing disallowing chimeric fragments ... [PASS] 464s Testing Allowing multi-mapped reads ... [PASS] 464s Testing not sorting input file ... [PASS] 464s Testing minimum overlapping length ... [PASS] 464s Testing minimum overlapping fraction ... [PASS] 464s Testing Largest Overlapping ... [PASS] 464s Testing paired-end distance ... [PASS] 464s Testing Read to position (5' end) ... [PASS] 464s Testing Read to position (3' end) ... [PASS] 464s Testing Read extension to the 3' end ... [PASS] 464s Testing Read extension to the 5' end ... [PASS] 464s Testing Low maxOPs value ... [PASS] 464s Testing minimum mapping quality ... [PASS] 464s Testing Ignoring duplicated reads ... [PASS] 464s Testing Fraction counting ... [PASS] 464s Testing Advanced fractions ... [PASS] 465s Testing Junction counting ... [PASS,PASS] 465s Skipping Junction counting (with genome). 465s Testing GTF format annotations ... [PASS] 465s Testing SAF format annotations ... [PASS] 465s Testing SAM format input ... [PASS] 465s Testing BAM format input ... [PASS] 465s Testing unstranded read summarization ... [PASS] 465s Testing stranded read summarization ... [PASS] 465s Testing reversely stranded read summarization ... [PASS] 465s Testing Ignoring duplicate fragments ... [PASS] 465s Testing Junction reads only ... [PASS] 465s Testing Exonic reads only ... [PASS] 465s 465s Testing intron_between ... [PASS] 465s Testing intron_between ... [PASS] 465s Testing intron_between ... [PASS] 465s Testing intron_between ... [PASS] 465s Testing across_genes ... [PASS] 465s Testing across_genes ... [PASS] 465s Testing across_genes ... [PASS] 465s Testing across_genes ... [PASS] 465s Testing across_intron ... [PASS] 465s Testing across_intron ... [PASS] 465s Testing across_intron ... [PASS] 465s Testing across_intron ... [PASS] 465s ../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b 465s Check the input format ... 466s 466s ========== _____ _ _ ____ _____ ______ _____ 466s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 466s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 466s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 466s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 466s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 466s v2.0.7 466s 466s //============================= exactSNP setting =============================\\ 466s || || 466s || Input file : test-in.BAM (BAM) || 466s || Output file : test-out.VCF || 466s || Reference genome : chr901.fa || 466s || Temp path : || 466s || || 466s || Threads : 1 || 466s || Min supporting reads : 1 || 466s || Min pct. of supporting reads : 0.0% || 466s || Min base quality score : 13 || 466s || Number of trimmed bases : 3 || 466s || || 466s || Q value cutoff : 10E-12.0 || 466s || P value upper bound : 0.00500 || 466s || Flanking windows size : 5 || 466s || || 466s \\============================================================================// 466s 466s //====================== Running (15-Mar-2025 17:06:41) ======================\\ 466s || || 466s || Split BAM file into result/temp-snps-002092-FA163EC6D2B3-* ... || 467s || processed block chr901@999950 by thread 1/1 [block number=1/1] || 467s || || 467s || Completed successfully. || 467s || || 467s \\============================================================================// 467s 467s //================================= Summary ==================================\\ 467s || || 467s || Processed reads : 50204 || 467s || Reported SNPs : 416 || 467s || Reported indels : 22 || 467s || || 467s || Running time : 0.0 minutes || 467s || || 467s \\============================================================================// 467s 467s  467s 467s ************************************************** 468s ************************************************** 468s *** *** 468s *** Test finished. *** 468s *** *** 468s *** Should there be any error, please visit *** 468s *** http://subread.sourceforge.net/ for more *** 468s *** information. *** 468s *** *** 468s ************************************************** 468s ************************************************** 468s 468s  468s 468s autopkgtest [17:06:43]: test subread-tests: -----------------------] 468s autopkgtest [17:06:43]: test subread-tests: - - - - - - - - - - results - - - - - - - - - - 468s subread-tests PASS 469s autopkgtest [17:06:44]: @@@@@@@@@@@@@@@@@@@@ summary 469s subread-tests PASS 487s nova [W] Using flock in prodstack6-arm64 487s flock: timeout while waiting to get lock 487s Creating nova instance adt-plucky-arm64-subread-20250315-165855-juju-7f2275-prod-proposed-migration-environment-2-3b08332a-cb95-4c01-a8d7-7c7d3c231577 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 487s nova [W] Timed out waiting for 9e7309ae-6845-4688-9af8-5be4aae8506f to get deleted.