trim.seqs sequence mismatch

I have run trim.seqs on two data sets for MiSeq and keep getting "sequence name mismatch btwn fatsa:______ and qual file: _________… however I am still getting output files. Should I be concerned about the output files from this command?


The mismatch error message is telling you that mothur is using the quality values from the sequence in named in the quality file to trim the sequence named in the fasta file. You do not want to use those outputs. I have modified mothur so that it will abort the command in this case and remove the output files.

Ah, I figured that might be the case, thank you!