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Hi @tseemann, this is related to the fasta export right? With bedtools

hi @wtscott31 From your output, I would say that adding the pathway 14DICHLORBENZDEG-PWY should have worked, whereas for the pathways PWY-6083, PWY-6081, PWY-6090, PWY-6091 no candidate reaction could be found...

hi @wtscott31 I'm sorry it took me some time, but there should be suitable candidate reactions for all the pathways by now! What needs to be checked is if chlorobenzene...

hi @bananabenana although this sounds interesting we do not see gapseq as an annotation software in the first place. nonetheless, it's a nice use case. I labeled it as a...

Many thanks for reviving this thread! Yes, adding oxalate makes sense, and I just committed it! The problem with the compounds @Erique29 provided some time ago was that many of...

at least the current debian version seems to have silva 138.1 see https://github.com/tseemann/barrnap/issues/59

hi @songmj86 Thank you for reporting the issue! It seems related to parallelization. Could you try running ``` $Tool doall -K 1 Bin10.fa ``` and check whether the error occurs...

top 10 produced compounds is indeed just a list of compounds with the highest outflux obtained from pFBA https://github.com/jotech/gapseq/blob/86f1896664998596ca0786d3fb14d23d0d6351bc/src/gf.suite.R#L668-L686 you should be able to reproduce with any cobra framework that...

Hi @mhjonathan Thank you for using gapseq :) I would argue that since microbial interactions are often context-dependent, defining the conditions under which you are looking for growth influences makes...

I agree, merging the growth media might work in your case! If you expect the interaction to be syntrophic (i.e., the product of A is strictly necessary for B's growth),...