azat-badretdin
commented
2 years ago Thank you for your report, @talberf !
The first mention of permanentFail in the log says:
[2022-10-12 11:37:11] INFO [job screen_evaluate] /pgap/output/debug/tmp-outdir/p1gtxuki$ screen_evaluate \
-ifmt \
seq-annot \
-tab \
/pgap/output/debug/tmpdir/ih18yvls/stgd2cbd2a6-0b4f-4c27-9df0-1bd14f7cc154/calls.tab
[2022-10-12 11:37:12] INFO [job screen_evaluate] Max memory used: 29MiB
[2022-10-12 11:37:12] WARNING [job screen_evaluate] exited with status: 1
[2022-10-12 11:37:12] WARNING [job screen_evaluate] completed permanentFail
That indicates to the problem in screening the input for something that does not belong.
Please have a look at output/calls.tab it will list nucleotides that have the problem. Please let us know if you need help interpreting it.
Cheers!
Describe the bug I am trying to annotate a genome that was assembled using illumina + nanopore reads in Unicycler. After a few minutes of running the pgap programme, it gives an error and stops.
To Reproduce I have ran it with other genomes before (and after) and it worked fine.
Software versions (please complete the following information):
Log Files cwltool.log.zip
Thank you!