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.