trim.seqs chokes on sequences with 0 length

I’ve been trying to process pyrotags and kept getting this error

sequence name mismatch btwn fasta: FX4HTZ101BFAV5 and qual file: >FX4HTZ101DKA6R

Turns out that FX4HTZ101DKA6R is a sequence with 0 length so I’ve deleted it. But it would be nice if mothur could delete seqs of 0 length, because it’s not easy to deal with these fasta and quality files that are too big to open in a text editor.



Thanks for the report, we’ll get on it for the next release.

Just curious…

did you delete the sequence in the fasta file before you ran it through MOTHUR? Was read FX4HTZ101DKA6R present in the qual file but not the fasta file initially?

I’m just wondering if having sequences in fasta and qual files in different order(or missing) will confuse mothur.



That sequence was in both files with no qual scores or sequence. So there were two lines with > next to each other.

like this:

bad seq
good seq

This will be fixed in 1.10.0, thanks for bringing it to our attention.


how did you generate the qual and fasta files?