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.