MACS2 error in Galaxy

Question

[haithem.barbour]

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

Answer 1

[Devon Ryan]

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.

[haithem.barbour]

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.