Hello everyone,

I was trying to run tophat in a local version of galaxy, but I got the following error:

gzip: stdout: Broken pipe
[Tue Jul 19 14:10:36 2011] Processing bowtie hits
Error: could not open pipe gzip -cd < ./tophat_out/tmp/left_kept_reads_missing.fq.z

It seems that when tophat is calling gzip, the pipe can not be open.

Can anyone suggest a fix to this problem?

Thanks,
Song Li
--
Postdoctoral Associate
Uwe Ohler Laboratory
Institute for Genome Sciences and Policy
101 Science Drive
CIEMAS 2171
Phone: 919-68-2124
Duke University