Question: MACS2 error in Galaxy
0
gravatar for haithem.barbour
3.7 years ago by
Canada
haithem.barbour0 wrote:

Hi,
i was trying to call peak using MACS2_callpeak on a ChIP-Seq data set.
The alignment went fine but the peak calling failed even though i can see
the results when i click on the "eye" icon but i can't do further
downstream analysis.
I am using the GenAP Galaxy instance.The error i think is basically that MACS2 couldn't find/write the build
file in the right directory. Please find attached the error report
generated by MACS2.

Thanks for your help.

Haithem

-------------------------------------------------------------------------------

.

.

INFO  @ Mon, 18 Jan 2016 11:03:05: #3 Call peaks for each chromosome...
INFO  @ Mon, 18 Jan 2016 13:44:55: #4 Write output xls file... MACS2_peaks.xls
INFO  @ Mon, 18 Jan 2016 13:44:55: #4 Write peak in narrowPeak format
file... MACS2_peaks.narrowPeak
INFO  @ Mon, 18 Jan 2016 13:44:55: #4 Write summits bed file...
MACS2_summits.bed
INFO  @ Mon, 18 Jan 2016 13:44:55: Done!
ERROR: Unable to read builds file: [Errno 2] No such file or
directory: '/nfs3_ib/...../ucsc/builds.txt'
ERROR: Unable to read builds file: [Errno 2] No such file or
directory: '/nfs3_ib/..../ucsc/publicbuilds.txt'
ERROR: Unable to read builds file: [Errno 2] No such file or
directory: '/nfs3_ib/...../ensembl/builds.txt'
ERROR: Unable to read builds file: [Errno 2] No such file or
directory: '/nfs3_ib/1......ncbi/builds.txt'
ERROR: Unable to read builds for site file
/nfs3_ib/...../ucsc/ucsc_build_sites.txt
ERROR: Unable to read builds for site file
/nfs3_ib/1..../gbrowse_build_sites.txt
----------------------------------------

chip-seq galaxy macs • 1.2k views
ADD COMMENTlink modified 3.7 years ago by Devon Ryan92k • written 3.7 years ago by haithem.barbour0
1
gravatar for Devon Ryan
3.7 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

You'll need to report the error to the server admin (click on the little "bug report" button on the errored job). Only he/she can fix the files, there's nothing you can do about this yourself.

ADD COMMENTlink written 3.7 years ago by Devon Ryan92k

Thanks, i have already sent the report to the admin and i thought i might be able to do something. I guess i'll just have to wait.

ADD REPLYlink written 3.7 years ago by haithem.barbour0
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