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conchoecia / odp

oxford dot plots
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segmentation fault following Matplotlib GUI usage warning - QObject::killTimer: Timers cannot be stopped from another thread #70

Open AdamVS opened 5 months ago

AdamVS commented 5 months ago

I am using the script for running the odp_basic test case, and I am receiving a segmentation fault following Matplotlib GUI usage warning, similar to the issue https://github.com/conchoecia/odp/issues/61. The exceptions are that I am running odp in Ubuntu LTS 20.04 with more memory (around 110 Gb, with 28 cores). A conda environment was created mamba create -n odp snakemake matplotlib pandas numpy seaborn diamond networkx and then also mamba install hmmer

The error starts after local rule plot_synteny_of_ALGs_plus_species and begins as a series : /home//bioinf/odp/tests/test_odp_basic/../../scripts/odp:1313: UserWarning: Starting a Matplotlib GUI outside of the main thread will likely fail. # make the black dots a little lighter

before: QObject::killTimer: Timers cannot be stopped from another thread Segmentation fault (core dumped)

Any ideas to troubleshoot and correct this would be greatly appreciated!

conchoecia commented 4 months ago

I have never hit a segfault error! Very interesting. Can you please tell me which version of python you are using, and which version of matplotlib?