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!