Hi All,
I just installed deeptools 3.5 onto my MacBook running Mojave. I am repeatedly getting a Segmentation fault: 11 on all the commands with deeptools. I am able to see the main help page of deeptools, but cannot run any of the other tools. Has this happened to anyone before, to do they know anything I can do to fix this issue?
Thank you!
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written
by
jjp55 •
1 answer
OK, so loading those packages didn't cause the segfault, which is good. Please create a new conda environment: conda create -n deeptools -c conda-forge -c bioconda deeptools=3.5.1 python=3.8 . Use that environment instead, since apparently there's an issue with the python installation you had been using.
Creating a new environment can get you out of many tough spots :)
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What sort of command is causing the segfault? How did you install deepTools? deepTools itself is just python, so it's very difficult for it to cause a segfault. My guess is that some dependency got installed incorrectly.
I have tried both the bamCoverage and computeMatrix and received the Segmentation fault message. I installed deepTools using
I have also tried to install with
$ conda install -c bioconda deeptoolsbut it was never able to install this way.Please try
conda install -c conda-forge -c bioconda deeptoolsinstead. Also, try to run the following first:I tried running
python -c "import pyBigWig; import numpy; import scipy;"followed byconda install -c conda-forge -c bioconda deeptoolsand I received the message: