Re: [galaxy-dev] broken-pipe error on NGS Fastq tools "clip"

That solved it! Thanks for pointing me in the right direction.

On Tue, Oct 4, 2011 at 1:19 AM, Peter Cock p.j.a.cock@googlemail.com wrote:

On Tue, Oct 4, 2011 at 1:33 AM, Colleen Doherty cdoherty@ucsd.edu wrote:

...

I am trying to set up a local instance. When running Clip adapter sequences I get the following error:

fastx_clipper: Invalid quality score value (char 'J' ord 74 quality value 41) on line 36 gzip: stdout: Broken pipe

I'm stuck on where to try to trouble-shoot this.

You need to upgrade to at least FASTX Toolkit v0.0.13, see: http://seqanswers.com/forums/showpost.php?p=49667&postcount=18

Old versions wrongly assumed PHRED quality scores would be at most 40.

Peter