Tophat Error: Broken Pipe

Question: Tophat Error: Broken Pipe

7.4 years ago by

Song Li • 10 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

alignment bowtie • 2.4k views

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modified 7.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.4 years ago by Song Li • 10

7.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/

ADD COMMENT • link written 7.4 years ago by Jennifer Hillman Jackson ♦ 25k

7.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Song, We have alpha support for Tophat v1.3.0 and it appears to work fine with Galaxy's Tophat wrappers. We'll upgrade and start full testing near term. For now, when running in a local instances, we do encourage users to try it and see if it meets their needs. Perhaps try with an uncompressed version of the same input file and see if that functions as expected or if the same error is given when used with the Galaxy wrappers? If you want to post testing details (Galaxy pull # from bitbucket, gzip, OS version and anything else you feel is relevant) after this sort of testing, the development team will use that information when full integration testing is performed. Perhaps others running local instances will also comment if you post these detailed testing results to the galaxy-dev@bx.psu.edu mailing list (will reach the primary external Galaxy development community). Thanks for using Galaxy! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/

ADD COMMENT • link written 7.4 years ago by Jennifer Hillman Jackson ♦ 25k

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