error:ordinary output of macs in stderr

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error:ordinary output of macs in stderr

韩宏庆

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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Re: error:ordinary output of macs in stderr

Björn Grüning-2
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_.3Cregex.3E.2C_and_.3Cexit_code.3E_tag_sets

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
>
>
> --------------------------------
>
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
>   http://galaxyproject.org/search/mailinglists/


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/