azat-badretdin
commented
1 year ago Thank you for your report, Beth!
You had a right idea to look for permanentFail signal in cwltool.log.
The relevant part preceding the first message of this kind (cwltool posts it after every single Russian Doll workflow that fails) 👍
[2023-05-25 16:50:24] INFO [job screen_evaluate] /tmp/ppfm9qbc$ screen_evaluate \
-ifmt \
seq-annot \
-tab \
/tmp/dfitdnmy/stgc5b0c534-4fbe-44cc-870e-14252a26a128/calls.tab
[2023-05-25 16:50:25] DEBUG Could not collect memory usage, job ended before monitoring began.
[2023-05-25 16:50:25] WARNING [job screen_evaluate] exited with status: 1
[2023-05-25 16:50:25] WARNING [job screen_evaluate] completed permanentFailYou should be able to find file called calls.tab with non-empty locations and target sequence specifications indicating to some contamination of your genome by adapter or vector sequences.
Hope this helps!
Congratulations with being the first user reporting an issue for our new May release!
-- Azat
bpeacock44
Hello,
I have been trying to run PGAP on an assembly file. PGAP runs the test data without any issues. The final error I get in the cwltool.log is: WARNING Final process status is permanentFail
Running on Linux (22.04.2-Ubuntu, x86_64 GNU/Linux)
It's not clear to me what the issue is arising from. I tried running it with and without the cpus option as suggested elsewhere
e.g. ./pgap.py -r -o strep_pgap_annotation contigs.yaml ./pgap.py -r —cpus 19 -o strep_pgap_annotation contigs.yaml ./pgap.py -r -o strep_pgap_annotation -g contigs.fna -s ‘Streptomyces’ ./pgap.py -r -c 19 -o strep_pgap_annotation -g contigs.fna -s ‘Streptomyces’
All produce the same result.
I've attached the contigs.yaml and submol.yaml files I use (I had to add "txt" to the end to upload) and the cwltool.log. Please let me know if there is more information I can provide. Thank you!!
contigs.yaml.txt submol.yaml.txt cwltool.log