Open rpetit3 opened 2 years ago
Hi @rpetit3 ! Thanks for getting in touch! I will take a look! It surely matters that percentage file is empty! i think the problem is the input files, you are using as input PlasmidFinder database, that is only rep and INC genes for detecting if there is a plasmid. PlasmidID needs as a database a set of COMPLETE plasmids in fasta format, because it tries to reconstruct the whole plasmids in the sample not only detect if there is one. In order to build the database you can create a custom one with sequences of your choice, or you can follow this steps: https://github.com/BU-ISCIII/plasmidID/wiki/Plasmid-Database
In any case I'm aware that the summary plasmid script may be a little bit buggy, so if you get any error, please tell me and I can check what is going on :)
Awesome! thank you for the update. I'll take a look at this and report back soon
I'm trying to run PlasmidID via the Bioconda release, and Am running into an issue with Pandas. Might be user error though!
Command Used
Here are the files used (added .txt so GitHub would allow upload) plasmidFinder_01_26_2018.fsa.txt SRX4563634.fna.txt
Update 1.
Doing some digging,
covered_df
might the issue. It looks like this:Going to play around with this some more
Update 2
Converted the ID to a string and now have this
Update 3
Looks like the dataframe is empty
Not sure if it matters but the
percentage_file
(e.g. *.coverage_adapted_clustered_percentage) does not exist