sff.multiple crash

Hello All,

I was using the sff.multiple command on 30 .sff files but mothur was crashing after the 7th .sff file. I read that this can happen when your sample reads aren’t well balanced.

My question is, when can I merge all the 30 files? I know the sff.multiple command takes the files through to trim.seqs, so does that mean I need to process each of my .sff files separately through the sff.info, trim.flows, shh.flows, and trim.seqs, before I can run the merge.files command?

Side note: I was able to save time by running all of the .sff files through the sff.info command by separating the names of each .sff file using dashes, e.g. file1.sff-file2.sff-file3.sff etc., but the dashes weren’t recognized as separators when I ran the trim.flows command so now I’m manually running 30 trim.flows commands.

Correct - you need to run everything through trim.seqs and then merge your fasta, names, and group files.