I’ve found that a couple of the visualization steps result in core dumped error and I haven’t been able to find any kind of fix elsewhere. Here are two examples of the errors:
7588 Aborted (core dumped) qiime demux summarize --i-data reads.qza --o-visualization reads.qzv
8820 Aborted (core dumped) qiime feature-table summarize --i-table repSeqsTable.qza --o-visualization repSeqsTable.qzv --m-sample-metadata-file $meta
I haven’t had a problem with any of the other visualization steps yet so they might be fine. We’re running this on a machine running Biolinux (built on Ubuntu 14.04) with 128 Gb of RAM. I installed a qiime2-2017.4 environment with Anaconda.
Thank you very much,
Hi @Shawn_Rupp! Sorry to hear you’re having troubles. By any chance are you running this on a headless server? If so, this looks like the kind of thing that matplotlib will complain about if it doesn’t have a display configured to use (for example, SSH without X forwarding). You can configure matplotlib to use an offscreen backend, see this forum post for an example. Hope that helps!
Thanks for the reply!
I was running this on a headless server, but I had the same problem on my desktop which is running Ubuntu 16.04. I was running into the error when I tried to generate the visualization (I ran a batch script to run through all of the steps and was going to examine the visualizations locally).
I configured matplotlib with:
echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
as you suggested and that seems to have solved the problem. Thanks for the help!
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