Question: deeptools bamCoverage error
gravatar for checkyodna
5 months ago by
checkyodna20 wrote:

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 --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/", 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/", 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/, 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/
  Expected in: flat namespace
 in /usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/

Any help would be greatly appreciated.

rna-seq • 285 views
ADD COMMENTlink modified 5 months ago by h.mon27k • written 5 months ago by checkyodna20

Can you try "import pyBigWig" in your python prompt? If that gives the same import error, you may try uninstalling and re-installing pyBigWig.

ADD REPLYlink written 5 months ago by Vitis2.2k

I would install conda and then get deeptools3 with it conda install deeptools. Takes care of all dependencies internally. Using environments you can keep your local python separated from the conda python3. Check the docs on conda. Did you install with brew?

ADD REPLYlink modified 5 months ago • written 5 months ago by ATpoint21k
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