Trackster and bedtools error
Dear all, As I was trying to do visualize my data set in trackster, I get the following error: /bin/sh: 1: bedtools: not found sort: fflush failed: standard output: Broken pipe sort: write error needLargeMem: trying to allocate 0 bytes (limit: 100000000000) When doing a sudo find / -name "bedtools" in my system, I get the following output: /usr/share/bedtools /usr/share/doc/bedtools Do I have bedtools installed in the wrong place? Thank you for your help, --Ricardo Perez
You'll need to make sure that bedtools is in your Galaxy user's path. Best, J. On Jul 9, 2013, at 6:40 PM, Perez, Ricardo wrote:
Dear all,
As I was trying to do visualize my data set in trackster, I get the following error:
/bin/sh: 1: bedtools: not found sort: fflush failed: standard output: Broken pipe sort: write error needLargeMem: trying to allocate 0 bytes (limit: 100000000000)
When doing a sudo find / -name "bedtools" in my system, I get the following output: /usr/share/bedtools /usr/share/doc/bedtools
Do I have bedtools installed in the wrong place?
Thank you for your help, --Ricardo Perez ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Thank you for your quick response. However, I have checked and bedtools are indeed in the galaxy path. When reviewind the log, I get the following: galaxy.jobs.runners.local DEBUG 2013-07-09 16:59:15,937 execution finished: grep -v '^#' /usr/local/galaxy/galaxy-dist/database/files/000/dataset_515.dat | sort -k1,1 | bedtools genomecov -bg -split -i stdin -g /usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len > temp.bg ; bedGraphToBigWig temp.bg /usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len /usr/local/galaxy/galaxy-dist/database/files/000/dataset_519.dat After reading the log, I ran the following command in my terminal: bedtools genomecov -bg -split -i stdin -g /usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len However this crashes. After looking in my computer, I find that bedtools do not contain the file genomecov. Is this an erroneous assumption of mine or have I installed something wrong? Than you for your time, --Ricardo Perez
bedtools genomecov -bg -split -i stdin -g /usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len
However this crashes. After looking in my computer, I find that bedtools do not contain the file genomecov. Is this an erroneous assumption of mine or have I installed something wrong?
genomecov is not a file, it is a parameter that indicates what operation to run. My guess is that you may have an old version of BEDtools installed; in this case, you'll need to update BEDtools. At minimum, BEDtools versions 2.15+ will work fine with Trackster/Galaxy. You can type this into your terminal to see the BEDtools version: bedtools --version Good luck, J.
participants (2)
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Jeremy Goecks -
Perez, Ricardo