[BUG] Failing to run some sequences

ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline

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[BUG] Failing to run some sequences #312

Closed jmemrava closed 3 weeks ago

jmemrava commented 3 weeks ago

I installed PGAP and am running it with the following command. However, I'm encountering issues where the output result files are not generated but specifically for certain sequences.

running

/opt/Software/pgap.py -r -g ERR4920664.fasta -s 'Pseudescherichia vulneris' -o ERR4920664 --cpus 15

cwltool.log file

cwltool.log

azat-badretdin commented 3 weeks ago

Thank you for you report, user @jmemrava !

Please have a look at file calls.tab you have some contamination in your assembly. You can overcome this by running with --ignore-all-errors flag.

jmemrava commented 3 weeks ago

Thanks @azat-badretdin ! I used the --ignore-all-errors flag and it works now.