Job starsolo_count.run_starsolo:NA:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.

[ymjzhang]

I am running StarSolo on SeqWell-prepared scRNAseq samples. This is the error message on Terro.bio:

Failures in starsolo_workflow.starsolo_count / index 0 / attempt 1
[0:{"message":"Workflow failed"
"causedBy":[
0:{
"message":"Job starsolo_count.run_starsolo:NA:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."}]}]

When I look into the logs, this is what I see:

Traceback (most recent call last):
File "", line 184, in
File "/usr/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['STAR', '--genomeDir', 'genome_ref', '--runThreadN', '16', '--outFileNamePrefix', 'result/', '--soloType', 'CB_UMI_Simple', '--soloCBstart', '1', '--soloCBlen', '12', '--soloUMIstart', '13', '--soloUMIlen', '8', '--outSAMtype', 'BAM', 'SortedByCoordinate', '--outSAMattributes', 'CR', 'UR', 'CY', 'UY', 'CB', 'UB', '--readFilesCommand', 'zcat', '--readFilesIn', '220209Lov_D22-122039_0/220209Lov_D22-122039_2_sequence.fastq.gz', '220209Lov_D22-122039_0/220209Lov_D22-122039_1_sequence.fastq.gz', '--soloCBwhitelist', 'None', '--soloBarcodeReadLength', '0', '--soloFeatures', 'Gene', 'GeneFull', 'Velocyto', '--soloCellFilter', 'CellRanger2.2', '8000', '0.99', '10']' died with <Signals.SIGSEGV: 11>.

I cannot think of how this sample is different from my other samples (which passed), and I do not understand the error message. Could anyone help me with troubleshooting what's going on?
Thank you.

[yihming]

Hi @ymjzhang ,

There are 2 possibilities:

1. Can you check "monitoring.log" in the execution folder of starsolo_count task of your job? It monitors the memory and disk space usage during the execution. If you see a high percentage (say > 95%), then probably the error is due to out of memory or disk space. If in this case, you would need to increase them, and resubmit your job.
2. Another issue could be due to STARsolo itself, as we've encountered similar issues with Velocyto feature set. If your job was running with star_version set to 2.7.10a, which is the latest version we provide, then you may create an issue in STAR repo, with log files specified in starsoloLogs output of your job attached.

[yihming]

Update: I've just made STAR v2.7.10b available for starsolo workflow. You may rerun your failed sample with this version (by setting star_version input to "2.7.10b"), and see if the issue could be fixed by this new version.