search

dib-lab / dammit

just annotate it, dammit!
http://dib-lab.github.io/dammit/
Other
88 stars 28 forks source link

`damit annotate` Exited with exit code 140 #187

Open CeciliaDeng opened 4 years ago

CeciliaDeng commented 4 years ago

Hi,

damit annotate completed ok to annotate 4 transcriptome assemblies but always failed for the other 2 transcriptomes. All 6 inputs were assembled using the same tool and in the same format (fasta). I tried several times to re-run the annotation. The failed message is usually "exit code 140", sometimes it's exit code 1 or 2. What do these exit codes mean? Is there anything wrong with the commands?

export TMPDIR=/path/to/project/tmp; dammit annotate $fasta --database-dir $dammitDB --full --busco-group eukaryota --n_threads 20 --output-dir $outputDir/R_eukaryota

Thank you.

eburgueno commented 4 years ago

Exit code 140 is the job scheduler killing the job because it exceeds the queue runlimit (24 hours in our case). You can send the jobs to a different queue and see if that makes a difference.

Would still be curious to know about the other exit codes.

camillescott commented 4 years ago

Thanks @eburgueno! I suspect that on occasion an individual program in the pipeline might be failing due to resource starvation just before the scheduler has the chance to kill the job, resulting in a code 1 or 2 rather than a 140.