plotHeatmap segmentation fault

[mmmmc...@gmail.com]

Hi all-
Since upgrading to deepTools 2.5, I am getting the following error with plotHeatmap:

/mnt/home/mcandr21/anaconda2/lib/python2.7/site-packages/subprocess32.py:472: RuntimeWarning: The _posixsubprocess module is not being used. Child process reliability may suffer if your program uses threads.
"program uses threads.", RuntimeWarning)
/var/spool/torque/mom_priv/jobs/41348378.mgr-04.i.SC: line 50: 30699 Segmentation fault (core dumped)

Has anyone else been getting this error? Do I need to upgrade one of the dependency packages?

[Fidel Ramirez]

That is very strange. I assume that the problem does not happen if you use a single processor right (-p 1).

Which exact version of python 2.7 do you have?

Best,
Fidel

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[mmmmc...@gmail.com]

I am using Python 2.7, but I don't think the -p argument works in plotHeatmap does it?

[mmmmc...@gmail.com]

Ahhhh sorry just saw you asked for specific version. I just reinstalled anaconda2, then used that to reinstall deepTools, but I am still getting the same error. My python 2.7 was installed with Anaconda 4.3.1 (64-bit).

[mmmmc...@gmail.com]

I should say more specifically that I am still getting a segmentation fault, though the

/mnt/home/mcandr21/anaconda2/lib/python2.7/site-packages/subprocess32.py:472: RuntimeWarning: The _posixsubprocess module is not being used. Child process reliability may suffer if your program uses threads.
"program uses threads.", RuntimeWarning)

portion of the error is no longer showing up.

[Vivek Bhardwaj]

The warning message was coming from subprocess module, so I guess updating the dependencies solved it. I can not reproduce the segfault on my data with plotHeatmap (v2.5.0.1). Can you try with another daatset?

Best Wishes

Vivek

--------

Vivek Bhardwaj

PhD Candidate | International Max Planck Research School 

Max Planck Institute of Immunobiology and Epigenetics

Stübeweg 51, Freiburg

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[mmmmc...@gmail.com]

It looks like this had something to do with matplotlib. I uninstalled matplotlib, then reinstalled an older version, and this seems to have corrected the issue

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[atoen...@gmail.com]

I had the same issue when using bamCoverage (deeptools3 installed with conda), and it turned out that there was some kind of conflicting version of subprocess32 that was installed by pip. pip uninstall subprocess32 solved the issue.