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OLC-Bioinformatics / ConFindr

Intra-species bacterial contamination detection
https://olc-bioinformatics.github.io/ConFindr/
MIT License
22 stars 8 forks source link

SamtoolsError #26

Closed mdabalkey closed 1 year ago

mdabalkey commented 2 years ago

Hello,

I have successfully processed several assemblies with Confindr but I have 15 records with an output similar to the indicated below.

sample001,Escherichia,ND,Pysam SamtoolsError,ND,ND,0,N

Could you please let me know the reason for this type of errors?

Thank you

adamkoziol commented 2 years ago

Hi! Sorry for the delay in getting back to you.

The SamtoolsError is a very general error indicating that the pysam library had an issue parsing the files. Unfortunately, it's not very descriptive. I've included a try/except SamtoolsError statement in the code to catch these errors, so that the entire program doesn't crash when they occur.

If you don't mind helping me debug your issue, could you either send me a link to an assembly and raw data set that returned that error, or send me the traceback if you remove the try/except?

Thanks, A

pcrxn commented 1 year ago

Closed due to inactivity.