Source: trinityrnaseq Version: 2.13.2+dfsg-3 Severity: serious Dear maintainer,
Somewhere around the end of January 2022, the autopkgtest of you package started to fail on amd64. Paul https://ci.debian.net/data/autopkgtest/testing/amd64/t/trinityrnaseq/19291359/log.gz All commands completed successfully. :-) ** Harvesting all assembled transcripts into a single multi-fasta file... Thursday, February 17, 2022: 04:50:39 CMD: find /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/Trinity.tmp * [Thu Feb 17 04:50:39 2022] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa 2 Error encountered:: <!---- CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa 2 2>tmp.5696.1645073439.stderr Errmsg: CMD: salmon --no-version-check index -t Trinity.tmp.fasta -i Trinity.tmp.fasta.salmon.idx -k 25 -p 2 > _salmon.7661.stderr 2>&1 CMD: salmon --no-version-check quant -i Trinity.tmp.fasta.salmon.idx -l U -r /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa -o salmon_outdir -p 2 --minAssignedFrags 1 --validateMappings > _salmon.7661.stderr 2>&1 Error, cmd: salmon --no-version-check quant -i Trinity.tmp.fasta.salmon.idx -l U -r /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa -o salmon_outdir -p 2 --minAssignedFrags 1 --validateMappings > _salmon.7661.stderr 2>&1 failed with msg: ### salmon (selective-alignment-based) v1.6.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { Trinity.tmp.fasta.salmon.idx } ### [ libType ] => { U } ### [ unmatedReads ] => { /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa } ### [ output ] => { salmon_outdir } ### [ threads ] => { 2 } ### [ minAssignedFrags ] => { 1 } ### [ validateMappings ] => { } Logs will be written to salmon_outdir/logs [2022-02-17 04:50:39.427] [jointLog] [info] setting maxHashResizeThreads to 2 ----------------------------------------- | Loading contig table | Time = 192.25 us ----------------------------------------- size = 637 ----------------------------------------- | Loading contig offsets | Time = 33.61 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 11.282 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 122.06 us ----------------------------------------- size = 246121 Number of ones: 636 Number of ones per inventory item: 512 Inventory entries filled: 2 [2022-02-17 04:50:39.427] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2022-02-17 04:50:39.427] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2022-02-17 04:50:39.427] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35. [2022-02-17 04:50:39.427] [jointLog] [info] parsing read library format [2022-02-17 04:50:39.427] [jointLog] [info] There is 1 library. [2022-02-17 04:50:39.427] [jointLog] [info] Loading pufferfish index [2022-02-17 04:50:39.427] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig boundaries | Time = 618.3 us ----------------------------------------- size = 246121 ----------------------------------------- | Loading sequence | Time = 49.733 us ----------------------------------------- size = 230857 ----------------------------------------- | Loading positions | Time = 398.03 us ----------------------------------------- size = 254072 ----------------------------------------- | Loading reference sequence | Time = 48.899 us ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 17.842 us ----------------------------------------- [2022-02-17 04:50:39.429] [jointLog] [info] done Segmentation fault Error, cmd: salmon --no-version-check quant -i Trinity.tmp.fasta.salmon.idx -l U -r /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa -o salmon_outdir -p 2 --minAssignedFrags 1 --validateMappings > _salmon.7661.stderr 2>&1 died with ret (35584) at /usr/lib/trinityrnaseq/PerlLib/Process_cmd.pm line 19. Process_cmd::process_cmd("salmon --no-version-check quant -i Trinity.tmp.fasta.salmon.i"...) called at /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl line 40 eval {...} called at /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl line 39 main::run_cmd_capture_stderr("salmon --no-version-check quant -i Trinity.tmp.fasta.salmon.i"..., "_salmon.7661.stderr") called at /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl line 27 ---> Error, cmd: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa 2 2>tmp.5696.1645073439.stderr died with ret 65280 at /usr/lib/trinityrnaseq/PerlLib/Pipeliner.pm line 187. Pipeliner::run(Pipeliner=HASH(0x56312e81af88)) called at /usr/lib/trinityrnaseq/Trinity line 4127 main::salmon_expr_filtering("Trinity.tmp.fasta", "/tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinity"..., "/tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinity"...) called at /usr/lib/trinityrnaseq/Trinity line 1460 make[1]: *** [Makefile:2: test] Error 255 make[1]: Leaving directory '/tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline' make: *** [Makefile:18: test] Error 2
