Jon Palmer
Jon Palmer
Or the EC annotation is wrong. I think it's eggnog but I can double check. At work I use ECPred to do this - it's quite slow but at least...
Currently in funannotate EC only coming from eggnog. So yes would be interesting to see how all three of those compare.
Thanks @fmobegi. Generally there is significant overlap. You would gain a lot more EC numbers using ECPred -- note the dashes are valid in NCBI for EC numbers (I think),...
Likely a few things. 1) GeneMark is not installed properly 2) Augustus 3.4 does not work with BUSCO in funannotate, use v3.3.3
Sorry for late response, so in your logfile I see that SNAP seems to be failing, I think on debian systems the conda version of snap is broken. You can...
It probably can be improved. I was never able to get exonerate to run with file like objects, ie so wouldn't need to write so many files. PR certainly welcome...
Haven't looked at the code in awhile, but if I didn't use seqio.index that would be easy. Not sure if that will ease the read requirements?
Well it should only run n processes (--cpus) at a time via the multiprocessing pool. So I don't see how it could be running 1000 at a time unless cpus=1000....
Okay, I just looked at it. Yes this code is rather old -- at the time I couldn't figure out how to pass kwargs properly to multiprocessing pool (ie pass...
I have something nearly done, give me a few more minutes. It might actually be slower but will allow for debugging the time. But I de-coupled the FASTA file generation...