Question: Error:Ordinary Output Of Macs In Stderr
0
韩宏庆 • 10 wrote:
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 ,errorAn 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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modified 4.9 years ago
by
Bjoern Gruening ♦ 5.1k
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written
4.9 years ago by
韩宏庆 • 10
