trim.seqs bugs

mothur bugs
1

Dear administrators,

I have just downloaded the MOTHUR version 1.8 for MacOSX 1.5 (64 bit version). I wanted to test the software with fasta file containing 1000 pyrotag sequences and a quality score file corresponding to these sequences. Below is the command that I used:

trim.seqs(fasta=test_1.fna,qfile=test_1.qual,qaverage=25,flip=T,pdiffs=2, qwindowaverage=35, qwindowsize=50, maxambig=0, maxhomop=8, processors=5)

This is how my input files look like

test_1.fna:

GE7GXPU01D8IQW length=46 xy=1620_0598 region=1 run=R_2010_04_06_17_16_27_
ACGGCGGTGTGTGCTCGTATCGCCGTCAATTCCTTAAGTTCTGAGC
GE7GXPU01CHW4V length=59 xy=0907_0365 region=1 run=R_2010_04_06_17_16_27_
ACGGGCGGTGTGTACCGTCAATTCATTTAAGTTTCTGAGCGGGCTGGCAAGGCGCATAG
GE7GXPU01AMYEY length=49 xy=0144_1320 region=1 run=R_2010_04_06_17_16_27_
ACGGCGGTGTGTGCCGTCAATTACTATTGTAGTTTCTTGAGCGGCGTGC
GE7GXPU01CHN93 length=58 xy=0904_1177 region=1 run=R_2010_04_06_17_16_27_
ACGGGCGGTGTGTGCCCGTCAATTCCTTAAGTTCTGAGCGGGCTGGCAAGGCGCATAG
GE7GXPU01C5JK2 length=57 xy=1176_0724 region=1 run=R_2010_04_06_17_16_27_
ACGGGCGGTGTGTGCCGTCAATTCATTGAGTTCTGAGCGGGCTGGCAAGGCGCATAG
GE7GXPU01D87LQ length=60 xy=1628_0044 region=1 run=R_2010_04_06_17_16_27_
ACGGGCGGTGTGTACCCGTCAATTCCTTTGAGTTTCTGAGCGGGCTGGCAAGGCGCATAG
GE7GXPU01C602E length=60 xy=1193_0404 region=1 run=R_2010_04_06_17_16_27_
ACGGGCGGTGTGTGCCCGTCAATTCCTTTGAGTTTCTGAGCGGGCTGGCAAGGCGCATAG
GE7GXPU01DP509 length=30 xy=1411_0379 region=1 run=R_2010_04_06_17_16_27_
ACGGCGGTGTGTGCCGTCAATTCATTTGAG
GE7GXPU01BJH35 length=62 xy=0515_0227 region=1 run=R_2010_04_06_17_16_27_
ACGGGCGGTGTGTACCCGTCAATTCCTTTAAGTTTCTGAGCGGGCTGGGCAAGGGCGCAT
AG

test_1.qual:

GE7GXPU01D8IQW length=46 xy=1620_0598 region=1 run=R_2010_04_06_17_16_27_
40 40 40 34 21 21 21 27 30 40 40 40 40 40 40 40 40 40 39 39 38 38 36 36 31 36 32 24 27 22 22 22 22 16 16 17 17 27 27 38 36 32 32 32 31 31
GE7GXPU01CHW4V length=59 xy=0907_0365 region=1 run=R_2010_04_06_17_16_27_
40 40 34 34 34 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 39 39 39 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
GE7GXPU01AMYEY length=49 xy=0144_1320 region=1 run=R_2010_04_06_17_16_27_
35 35 32 25 18 16 16 24 23 27 28 24 20 16 16 17 19 11 12 12 12 12 11 19 11 14 12 12 14 16 19 14 11 11 11 14 11 13 19 22 23 22 20 20 28 21 19 14 14
GE7GXPU01CHN93 length=58 xy=0904_1177 region=1 run=R_2010_04_06_17_16_27_
30 20 20 19 19 27 15 15 34 32 40 40 32 27 15 15 15 27 27 27 18 18 18 18 18 18 13 13 14 14 27 18 23 27 32 36 36 32 31 16 18 18 32 36 40 40 40 36 36 36 36 40 40 40 40 40 40 40
GE7GXPU01C5JK2 length=57 xy=1176_0724 region=1 run=R_2010_04_06_17_16_27_
30 27 21 21 21 30 22 34 40 40 40 40 40 40 40 40 40 40 39 34 34 33 33 32 27 22 22 27 32 27 20 20 27 27 36 36 27 19 15 15 15 27 24 24 24 32 31 29 29 31 38 36 36 36 40 40 40
GE7GXPU01D87LQ length=60 xy=1628_0044 region=1 run=R_2010_04_06_17_16_27_
40 40 39 39 39 40 40 40 40 40 40 40 40 40 39 39 39 40 39 40 39 39 40 40 40 40 39 39 39 40 40 40 38 38 38 39 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
GE7GXPU01C602E length=60 xy=1193_0404 region=1 run=R_2010_04_06_17_16_27_
40 40 39 39 39 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 39 39 39 39 39 39 39 40 40 40 39 39 39 40 40 40 40 40 40 39 39 39 35 30 30 30 30 39 40 40 40 40 40 40 40 40 40 40
GE7GXPU01DP509 length=30 xy=1411_0379 region=1 run=R_2010_04_06_17_16_27_
35 26 26 26 27 24 24 27 36 40 40 40 40 40 40 40 40 33 34 34 33 33 36 32 17 17 17 32 32 19
GE7GXPU01BJH35 length=62 xy=0515_0227 region=1 run=R_2010_04_06_17_16_27_
40 40 39 39 39 40 40 40 40 40 40 40 40 40 39 39 39 40 40 35 34 34 40 40 40 36 31 27 27 35 27 25 13 13 13 25 25 32 32 25 25 13 13 13 25 30 14 14 14 24 24 24 24 24 31 31 22 29 33 33
36 38

For some reason, this command fails to execute, even after waiting for 10 minutes (and it also takes up a lot of memory, slowing down my machine quite a bit). Is there something I need to do to the input files that will prevent from such event from occurring? Your advice would be much appreciated. Thank you.

Young

2

I have just sent the fasta and quality files to mothur.bugs@gmail.com

Young

3

Thanks for sending us your files; they were very helpful in finding the problem. I noticed when I ran your files that the quality files last line ended without a line return. mothur’s read of the quality file expected a line return. Thanks for bringing this bug to our attention. The fix will be part of version 1.19.0.