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alexstaj / cutadapt

Automatically exported from code.google.com/p/cutadapt
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"ValueError: Length of quality sequence and length of read do not match (81+0!=80)" #9

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
I have a fastq file with 80 nt long reads. The quality lines also have a length 
of 80 but cutadapt is reporting that they are not equal.  I have run other 
adapter sequence removing programs that have run just fine. What can I do to 
fix this?

Original issue reported on code.google.com by gregorym...@gmail.com on 14 Feb 2011 at 7:03

GoogleCodeExporter commented 9 years ago 
This sounds like a DOS/Windows line end issue. Your FASTQ file may have DOS 
line endings. Please try to open the file lib/cutadapt/fasta.py and replace the 
line

qualities = line[:-1]

(around line 26) with the line

qualities = line.rstrip("\n\r")

and re-try.

Original comment by marcel.m...@tu-dortmund.de on 15 Feb 2011 at 7:58

GoogleCodeExporter commented 9 years ago 
Thank you very much.  That worked perfectly.

Original comment by gregorym...@gmail.com on 15 Feb 2011 at 8:21

GoogleCodeExporter commented 9 years ago 
Great, then the next release will include this change. Thanks for the report!

Original comment by marcel.m...@tu-dortmund.de on 16 Feb 2011 at 9:44