broken-pipe error on NGS Fastq tools "clip"
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. This is on groomed fastq data in my history. I have the same error on other datasets. Other tools (Bowtie, FastQC) work on this dataset. I'm confused why it is gzip (but I clearly don't understand how Galaxy stores the data). Thanks for any suggestions!
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
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
participants (2)
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Colleen Doherty -
Peter Cock