search

ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline
Other
301 stars 89 forks source link

Annotation fails #225

Closed talberf closed 1 year ago

talberf commented 1 year ago

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.

CH409_fail

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!

azat-badretdin commented 1 year 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!