Question: EPIC Error calculating readlength
0
gravatar for ariel.balter
2.1 years ago by
ariel.balter130
ariel.balter130 wrote:

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
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by ariel.balter130
0
gravatar for Devon Ryan
2.1 years ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

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

ADD COMMENTlink written 2.1 years ago by Devon Ryan86k

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 REPLYlink written 2.1 years ago by ariel.balter130

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

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Devon Ryan86k
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