Closed michellescribner closed 5 months ago
Never seen this before. Looks like an issue with plasmidfinder code itself. Here's the relevant error:
Traceback (most recent call last):
File "/plasmidfinder/plasmidfinder.py", line 360, in <module>
min_cov, threshold, method_path, cut_off=False)
File "/usr/local/lib/python3.5/dist-packages/cgecore/blaster/blaster.py", line 242, in __init__
hit)
File "/usr/local/lib/python3.5/dist-packages/cgecore/blaster/blaster.py", line 508, in calculate_new_length
new_start = int(gene_results[split]['sbjct_start'])
KeyError: 'contig00053 len=17204 cov=50.7 corr=0 origname=Contig_45_50.6781_pilon sw=shovill-skesa/1.1.0 date=20231218:7898..8044:rep1_9_repE(pKL0018)_AB290882:9.456740'
No plasmids detected in database
Perhaps you could try switching to spades
as the assembly algorithm? FASTA headers will be different, so maybe that will help? 🤷
Good call, I just gave that a whirl: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Scribner_Sandbox/job_history/7a0e8786-bb73-4874-94ac-017acdaea0f3
I was thinking that the plasmidfinder web tool would fail if it was a fasta header issue but I'm not sure if the web tool is using the same exact software/db as our implementation
FYI I think it's safe to assume that the version of plasmidfinder on the webtool is more recent than the one used in our docker image.
If this is an old bug that has already been addressed in the plasmidfinder code, then it would be a good idea to update the docker image to the most recent version and subsequently update the WDL to use the new one.
In the absence of a more recent version of plasmidfinder, in the meantime we can add a boolean to TheiaProk to turn off plasmidfinder.
For example:
call_plasmidfinder
= true
:bug:
A collaborator reported repeated TheiaProk failures for Enterococcus samples at the plasmidfinder task: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Scribner_Sandbox/job_history/6d7a5682-0e30-44b7-8d66-8b9eac45bbf0
Cause of the issue is not clear to me. The same assembly run through the PlasmidFinder webtool successfully finished and detected plasmids but took several days to run.
:pencil: Describe the Issue
:repeat: How to Reproduce
miniwdl
orcromwell
?:fishing_pole_and_fish: Expected Behavior
:floppy_disk: Version Information
:information_source: Additional Information