EPIC Error calculating readlength
1
0
Entering edit mode
5.7 years ago
ariel.balter ▴ 190

Cross-posted here. Hoping for quick answer!

Update:

Getting same error with their test data from the examples.

Original post:

I'm getting

# epic -t chip_A-sortsam.bam -c input_A-sortsam.bam -fs 300 (File: epic, Log level: INFO, Time: Thu, 06 Oct 2016 06:56:24 )
cat: write error: Broken pipe
Used first 10000 reads of chip_A-sortsam.bam to estimate a median read length of nan
Mean readlength: nan, max readlength: nan, min readlength: nan. (File: find_readlength, Log level: INFO, Time: Thu, 06 Oct 2016 06:56:25 )
# epic -t chip_A-sortsam.bam -c input_A-sortsam.bam -fs 300
Traceback (most recent call last):
  File "/home/users/balter/miniconda2/bin/epic", line 4, in <module>
    __import__('pkg_resources').run_script('bioepic==0.1.17', 'epic')
  File "/home/users/balter/miniconda2/lib/python2.7/site-packages/setuptools-23.0.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script
  File "/home/users/balter/miniconda2/lib/python2.7/site-packages/setuptools-23.0.0-py2.7.egg/pkg_resources/__init__.py", line 1504, in run_script
  File "/home/users/balter/miniconda2/lib/python2.7/site-packages/bioepic-0.1.17-py2.7.egg-info/scripts/epic", line 190, in <module>
    closest_readlength = get_closest_readlength(estimated_readlength)
  File "/home/users/balter/miniconda2/lib/python2.7/site-packages/epic/utils/find_readlength.py", line 63, in get_closest_readlength
    if d == min_difference][0]
IndexError: list index out of range

BAM files:

ls -l
total 6622033
-rw-rw-r-- 1 balter CompBio 3387571391 Oct  6 05:59 chip_A-sortsam.bam
-rw-rw-r-- 1 balter CompBio 3387571391 Oct  6 06:34 input_A-sortsam.bam
epic peak calling ChIP-Seq software error • 1.7k views
ADD COMMENT
0
Entering edit mode
5.7 years ago

Note the file format that it takes as input...

ADD COMMENT
0
Entering edit mode

Oh golly! It only takes bed files? That seems so odd. Why not just check and run bam to bed. I'll give it a shot...

ADD REPLY
0
Entering edit mode

I presume this is what SICER takes, though I agree it'd be a nice enhancement.

ADD REPLY

Login before adding your answer.

Traffic: 1911 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6