Hello Song Li,

The file extension seems to be a mismatch.

file.gz <- "gzip" utility

Exploring the use of gunzip or zcat are options to restore a "file.z".

Hopefully this helps,

Jen
Galaxy team

On 7/19/11 11:52 AM, Song Li wrote:
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



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