Hi Han, you can filter the output of every tool and react on it with the stdio tag in Galaxy. for more information please have a look at the wiki page: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cstdio.3E.2C_... Cheers, Bjoern

Hello, galaxy users and developers,

I wrote a perl script conducting saturation analysis which called macs several times.

The tool's output was right but ,

error An error occurred with this dataset:INFO @ Sat, 18 Jan 2014 21:46:33: # ARGUMENTS LIST: # name = /usr/local/galaxy-dist/database/job_working_directory/000/0.output # format = BED # ChIP-seq file = 0.test.bed # control file = 0.control.bed # effective genome size = 2.70e+09 # tag size = 2

Tool execution generated the following error message:

INFO @ Sat, 18 Jan 2014 21:46:33: # ARGUMENTS LIST: # name = /usr/local/galaxy-dist/database/job_working_directory/000/0.output # format = BED # ChIP-seq file = 0.test.bed # control file = 0.control.bed # effective genome size = 2.70e+09 # tag size = 28 # band width = 300 # model fold = 16 # pvalue cutoff = 1.00e-05 # Ranges for calculating regional lambda are : peak_region,1000,5000,10000 INFO @ Sat, 18 Jan 2014 21:46:33: #1 read tag files... INFO @ Sat, 18 Jan 2014 21:46:33: #1 read treatment tags... INFO @ Sat, 18 Jan 2014 21:46:37: #1.2 read input tags... INFO @ Sat, 18 Jan 2014 21:46:39: #1 Background Redundant rate: 0.04 INFO @ Sat, 18 Jan 2014 21:46:39: #1 finished! INFO @ Sat, 18 Jan 2014 21:46:39: #2 Build Peak Model... INFO @ Sat, 18 Jan 2014 21:46:47: #2 number of paired peaks: 11875 INFO @ Sat, 18 Jan 2014 21:46:47: #2 finished! INFO @ Sat, 18 Jan 2014 21:46:47: #2.2 Generate R script for model : /usr/local/galaxy-dist/database/job_working_directory/000/0.output_model.r INFO @ Sat, 18 Jan 2014 21:46:47: #3 Call peaks... INFO @ Sat, 18 Jan 2014 21:46:47: #3 shift treatment data INFO @ Sat, 18 Jan 2014 21:46:47: #3 merge +/- strand of treatment data INFO @ Sat, 18 Jan 2014 21:46:47: #3 call peak candidates INFO @ Sat, 18 Jan 2014 21:46:48: #3 shift control data INFO @ Sat, 18 Jan 2014 21:46:48: #3 merge +/- strand of control data INFO @ Sat, 18 Jan 2014 21:46:48: #3 call negative peak candidates INFO @ Sat, 18 Jan 2014 21:46:48: #3 use control data to filter peak candidates... INFO @ Sat, 18 Jan 2014 21:46:48: #3 Finally, 2003 peaks are called! INFO @ Sat, 18 Jan 2014 21:46:48: #3 find negative peaks by reversing treat and control INFO @ Sat, 18 Jan 2014 21:46:49: #3 Finally, 120 peaks are called! INFO @ Sat, 18 Jan 2014 21:46:49: #4 Write output xls file... /usr/local/galaxy-dist/database/job_working_directory/000/0.output_peaks.xls INFO @ Sat, 18 Jan 2014 21:46:49: #4 Write output bed file... /usr/local/galaxy-dist/database/job_working_directory/000/0.output_peaks.bed INFO @ Sat, 18 Jan 2014 21:46:49: #4 Write output xls file for negative peaks... /usr/local/galaxy-dist/database/job_working_directory/000/0.output_negative_peaks.xls INFO @ Sat, 18 Jan 2014 21:46:49: #5 Done! Check the output files!

Just ordinary macs output, we see it in galaxy-macs report. The only problem is that they're in stderr. With this error I cannot do other works with the output of this tool.

How can I deal with it?

Thanks!

-Han

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