"ValueError: Length of quality sequence and length of read do not match (81+0!=80)"

[marcelm]

From gregorym...@gmail.com on February 14, 2011 20:03:17

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: http://code.google.com/p/cutadapt/issues/detail?id=9

[marcelm]

From marcel.m...@tu-dortmund.de on February 15, 2011 11:58:16

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.

[marcelm]

From gregorym...@gmail.com on February 15, 2011 12:21:37

Thank you very much. That worked perfectly.

[marcelm]

From marcel.m...@tu-dortmund.de on February 16, 2011 01:44:44

Great, then the next release will include this change. Thanks for the report!

Status: Verified