[Debian-med-packaging] Bug#1006336: trinityrnaseq: autopkgtest regression in testing: segmentation fault

[Paul Gevers]

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