deeptools 3.5 Segmentation fault:11

Question

[jjp55]

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!

[Devon Ryan]

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.

[jjp55]

I have tried both the bamCoverage and computeMatrix and received the Segmentation fault message. I installed deepTools using

$ pip install deeptools

I have also tried to install with $ conda install -c bioconda deeptools but it was never able to install this way.

[Devon Ryan]

Please try conda install -c conda-forge -c bioconda deeptools instead. Also, try to run the following first:

python -c "import pyBigWig; import numpy; import scipy;"

[jjp55]

I tried running python -c "import pyBigWig; import numpy; import scipy;" followed by conda install -c conda-forge -c bioconda deeptools and I received the message:

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

Answer 1

[Devon Ryan]

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.

[jjp55]

That solved the problem! Thank you!

[Devon Ryan]

Creating a new environment can get you out of many tough spots :)