Issues with trim.seqs qtrim parameter

Commands in mothur
1

Hi!

I seem to be having a problem using the qtrim parameter in the trim.seqs command. When I run it without the qtrim parameter – allowing it to scrap all files that don’t meet the qthreshold – I get plenty of reads in my .trim.fasta file. However, if I try to force triming using qtrim=true, my .trim.fasta file is empty! Am I doing something wrong here?

Thanks!
Lizzy

mothur > trim.seqs(fasta=raw_pinkB.fasta, qfile=raw_pinkB.qual, qthreshold=5)
mothur > summary.seqs(fasta=raw_pinkB.trim.fasta)

                Start   End     NBases  Ambigs  Polymer
Minimum:        0       0       0       0       1
2.5%-tile:      1       58      58      0       3
25%-tile:       1       271     271     0       4
Median:         1       383     383     0       5
75%-tile:       1       458     458     0       6
97.5%-tile:     1       517     517     0       8
Maximum:        1       614     614     0       31
# of Seqs:      257983

Output File Name:
raw_pinkB.trim.fasta.summary

mothur > trim.seqs(fasta=raw_pinkB.fasta, qfile=raw_pinkB.qual, qthreshold=5,qtrim=true)
mothur > summary.seqs(fasta=raw_pinkB.trim.fasta)

[ERROR]: raw_pinkB.trim.fasta is blank. Please correct.
Error in reading your fastafile, at position -1. Blank name.
Segmentation fault
2

Could you send your inputfiles and logfile to mothur.bugs@gmail.com?

3

Thanks for bringing this bug to our attention. In version 1.15.0, we made some changes to the internal workings of the trim.seqs command and unfortunately added and indexing error, :oops: . The fix will be part of 1.16.0.