help with segmentation fault deeptools

Hi I'm having a problem with running deeptools on an iMac. It's a MacOS 10.15.6 and I've installed anaconda and deeptools; which all seems to be there. From other help suggestions I have

campbell.1933@campbell-iMac BW % conda list |grep python
ipython                   7.16.1           py38h5ca1d4c_0  
ipython_genutils          0.2.0                    py38_0  
msgpack-python            1.0.0            py38h04f5b5a_1  
python                    3.8.3                h26836e1_2  
python-dateutil           2.8.1                      py_0  
python-jsonrpc-server     0.3.4                      py_1  
python-language-server    0.34.1                   py38_0  
python-libarchive-c       2.9                        py_0  
python.app                2                       py38_10

also deeptools seems to be there, as at the prompt it shows the list of all the tools available. But whatever command I try to run I get

(base) campbell.1933@campbell-iMac BW % computeMatrix -S DCIS.AIB1.1.bw -R clusters.MCFDCIS.AIB1.Input.bed -b 1000 -o matrix
zsh: segmentation fault  computeMatrix -S DCIS.AIB1.1.bw -R clusters.MCFDCIS.AIB1.Input.bed -b 1000 -o

Any suggestions very gratefully received! thanks Moray

chip-seq software error deeptools

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written 5.9 years ago by campbell.1933 •

Some dependency must be installed incorrectly or have an issue. Try making a new conda environment and see if that fixes the issue.

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written 5.9 years ago by Devon Ryan

reinstall anaconda?

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written 5.9 years ago by campbell.1933 •

reinstalled python version and used brew and pyenv to make 3.8.5 default and then installed anaconda3. Different errors that seem much more specific! Any thoughts? Please

Traceback (most recent call last):
  File "/Users/campbell.1933/.pyenv/versions/3.8.5/bin/bamCoverage", line 5, in <module>
    from deeptools.bamCoverage import main
  File "/Users/campbell.1933/.pyenv/versions/3.8.5/lib/python3.8/site-packages/deeptools/bamCoverage.py", line 8, in <module>
    from deeptools import writeBedGraph  # This should be made directly into a bigWig
  File "/Users/campbell.1933/.pyenv/versions/3.8.5/lib/python3.8/site-packages/deeptools/writeBedGraph.py", line 8, in <module>
    from deeptools import mapReduce
  File "/Users/campbell.1933/.pyenv/versions/3.8.5/lib/python3.8/site-packages/deeptools/mapReduce.py", line 2, in <module>
    from deeptoolsintervals import GTF
  File "/Users/campbell.1933/.pyenv/versions/3.8.5/lib/python3.8/site-packages/deeptoolsintervals/__init__.py", line 1, in <module>
    from deeptoolsintervals.parse import GTF
  File "/Users/campbell.1933/.pyenv/versions/3.8.5/lib/python3.8/site-packages/deeptoolsintervals/parse.py", line 3, in <module>
    from deeptoolsintervals import tree
ImportError: dlopen(/Users/campbell.1933/.pyenv/versions/3.8.5/lib/python3.8/site-packages/deeptoolsintervals/tree.cpython-38-darwin.so, 2): Library not loaded: @rpath/libpython3.8.dylib
  Referenced from: /Users/campbell.1933/.pyenv/versions/3.8.5/lib/python3.8/site-packages/deeptoolsintervals/tree.cpython-38-darwin.so
  Reason: image not found

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updated 5.9 years ago by GenoMax

• written 5.9 years ago by campbell.1933 •

For some reason the python 3.8 library couldn't be found. It's obviously somewhere on your system, but I wonder if there's some obscure environment variable that's set that's messing up the linker on your system.

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written 5.9 years ago by Devon Ryan

0 answers

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