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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