[BUG] anvi-merge error (can I put multiple contigs.db in the code?) about anvio

[ivagljiva]

Hi @soojunglee98, you cannot merge multiple contigs DBs, and you also cannot merge profile DBs that are not associated with the same contigs database. Merging profiles only works if the read recruitment for each was done on the same reference contigs.

So if you want to merge everything into one contigs DB-profile DB pair, you would need to start your workflow from the beginning by combining all contigs into the same reference FASTA, create a single contigs DB from that reference, and then do read recruitment on that reference to get several profile DBs all linked to the same set of contigs, and then run anvi-merge.

I hope this makes sense.

(The error from anvi-merge is happening because you cannot provide more than one contigs db to the -c parameter)