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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