Deleted:deeptools bamCoverage error
0
0
Entering edit mode
5.1 years ago
checkyodna ▴ 60

I am encountering a problem when trying to use deeptools (version 2.5.4) and I cannot find any help online. My aim is to convert a BAM file to a bigWig file to visualise tracks on UCSC genome browser. I am using the following command:

bamCoverage -b Striatum_W2_UCSCindex.bam -o Striatum_W2.bw --normalizeUsing RPKM

The error I am getting might be related to my python path (I have blindly attempted a few commands as I am new to bioinformatics) and the full error message is here;

Traceback (most recent call last):
  File "/usr/local/bin/bamCoverage", line 4, in <module>
    from deeptools.bamCoverage import main
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/deeptools/bamCoverage.py", line 8, in <module>
    from deeptools import writeBedGraph  # This should be made directly into a bigWig
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/deeptools/writeBedGraph.py", line 5, in <module>
    import pyBigWig
ImportError: dlopen(/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pyBigWig.so, 2): Symbol not found: _kSecClass
  Referenced from: /usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pyBigWig.so
  Expected in: flat namespace
 in /usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pyBigWig.so

Any help would be greatly appreciated.

RNA-Seq • 3.3k views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 1563 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