Question: Troubleshooting MACS bdgcmp
0
gravatar for mparker2
4.2 years ago by
mparker220
Sheffield
mparker220 wrote:

I am trying to generate a log FE Bedgraph file from some chip seq data. I already have some bedgraph tracks for the control and treated samples, but when I run MACS bdgcmp for the two I get an error message. Can anyone enlighten me as to how to fix this:

macs2 bdgcmp -t /home/matthew/Desktop/Projects/raw_data/histone_chip/HTR5_treat_afterfiting_all.bdg.gz -c /home/matthew/Desktop/Projects/raw_data/histone_chip/HTR5_control_afterfiting_all.bdg.gz --outdir /home/matthew/Desktop/Projects/raw_data/histone_chip/ --o-prefix HTR5_FE -m logFE
INFO  @ Fri, 19 Jun 2015 14:48:14: Read and build treatment bedGraph...
Traceback (most recent call last):
  File "/usr/local/bin/macs2", line 4, in <module>
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150420', 'macs2')
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 729, in run_script
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 1649, in run_script
  File "/usr/local/lib/python2.7/dist-packages/MACS2-2.1.0.20150420-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in <module>
    
  File "/usr/local/lib/python2.7/dist-packages/MACS2-2.1.0.20150420-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 72, in main
    
  File "build/bdist.linux-x86_64/egg/MACS2/bdgcmp_cmd.py", line 40, in run
  File "MACS2/IO/BedGraphIO.pyx", line 108, in MACS2.IO.BedGraphIO.bedGraphIO.build_bdgtrack (MACS2/IO/BedGraphIO.c:1245)
IndexError: list index out of range

 

chip-seq • 1.7k views
ADD COMMENTlink written 4.2 years ago by mparker220
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1014 users visited in the last hour