Cutadapt value error

[GoogleCodeExporter]

I am running trim_galore to quality trim sets of paired end illumina sequence. 
I have two files, a forward and a reverse (R1, R2). When I run them using the 
--paired command in trim_galore through an ssh connection to our server, the 
"forward" fq file seems to run fine, but the "reverse" fq file gives the 
following error:

File "/admin/software/precise/static/cutadapt-1.1/cutadapt/seqio.py", line 280, 
in __iter__
    raise ValueError("Length of quality sequence and length of read do not match (%d+%d!=%d)" % (len(qualities), lengthdiff, len(sequence)))
ValueError: Length of quality sequence and length of read do not match 
(100+0!=1630)

Is there any reason why this would be? 
Thanks for your help!

Original issue reported on code.google.com by ktoma...@gmail.com on 8 Nov 2012 at 11:39

[GoogleCodeExporter]

One record in your FASTQ file seems to contain 100 quality values but 1630 
nucleotides. I'm quie certain that the file is corrupt and that this is not a 
problem with cutadapt. It could also be an issue with DOS vs. Unix line 
endings, I'm not sure. To reproduce the problem, I would need the cutadapt 
command-line parameters that were used and a small example file that shows the 
problem. If that is not available, I ask you to report the problem to the 
trim_galore developer.

Original comment by marcel.m...@tu-dortmund.de on 9 Nov 2012 at 8:13

[GoogleCodeExporter]

Any news? I'd like to close this issue unless there's further information.

Original comment by marcel.m...@tu-dortmund.de on 13 Nov 2012 at 10:11

[GoogleCodeExporter]

Original comment by marcel.m...@tu-dortmund.de on 20 Nov 2012 at 8:00

• Changed state: WontFix