How to reuse prodigal output from independent checkM run

[shiraz-shah]

Thanks for making this great tool!!

Question:
If I've already run CheckM previously, can I reuse its prodigal-output for dRep?

I've already make a --genomeInfo CSV file with CheckM completion and contamination stats, but dRep still wants to run prodigal.

I'd like to avoid installing and running prodigal because the ORFs it calls could change.

Also, why does dRep need prodigal when its comparisons are based on ANI? Can I disable this part of its workflow if my bins are already qc'd?

[MrOlm]

Interesting. dRep shouldn't run prodigal if you already are giving it genomeInfo; it should only run prodigal for checkM. Can you check the logs and confirm that it's reading your checkM results properly?

Also- you can always run in compare mode and dereplicate manually if you want to avoid this issue altogether.

Best,
Matt

[shiraz-shah]

Thanks. Yes, that's the route I ended up going. However,compare crashes for now because it can't run FastANI.

I've opened another issue about pip install drep not installing all required dependencies. Installing FastANI manually makes dRep unable to use FastANI.