Special characters in genome name broke the samtools depth step

[sgsutcliffe]

Excited to use this tool. I think it will help me automate the process of determining active prophages.

I've got a bacterial genome I ran VIBRANT on whose name is 'ENA|CP000721|CP000721.1 Clostridium beijerinckii NCIMB 8052, complete genome'

Sam shortens it to 'ENA|CP000721|CP000721.1' due to space (as you've mentioned in your instructions). So dealt with that in the prophage coordinate file.

When I ran it I get '/bin/sh: CP000721: command not found'
Then I get the help output for samtools depth. So I am thinking the name of the genome is causing the bug.

So I shortened 'ENA|CP000721|CP000721.1' to CP000721 on all my files, thinking the '|' character was causing the error. I am not too proficient in python.

This then worked fine. We got the active prophages we were looking for. Don't know if this is too basic of an issue to address, but I thought I would flag just in case it is an easy fix.

Thanks for releasing this great tool!

[KrisKieft]

Hi,

I've seen issues with the pipe '|' symbol before and overlooked implementing a solution into PropagAtE. Thank you for pointing this out and I'll push a solution in a future version.

Kris