Hi
I just realized that Metabat outputs hidden bin files in fasta format in the output directory meant for the final bins. This messes up the input to checkm
Are these hidden files temporary files that did not get removed when metabat finished its run?
No, I did not use the --unbinned option. By hidden files, I mean those that are .bin.fa in the output directory
The output directory seems to consist of a number of these hidden files in addition to the correct number of bin files that Metabat reported at the end of its run
It seems weird. MetaBAT doesn't keep any temporary fasta files. Can you share your command line as well as data to reproduce it?
What do you mean by 'hidden files'? Did you use '--unbinned' option? In this case, it will produce unbinned contigs as a fasta file. Otherwise, I don't think MetaBAT produces any temporary bins.