Hi @Alex_14262! Which QIIME 2 release are you using? The matplotlib backend issue should be resolved in QIIME 2 releases 2017.9 and later.
You could try setting an environment variable instead of using a matplotlib config file. You may need to first remove the config file you created for the environment variable to take effect.
export MPLBACKEND='Agg'
You can run the above command in your terminal, or put it in your ~/.bashrc file for it to take effect each time you open a new terminal window.
If that doesn’t work, and you’re using a release of QIIME 2 that is 2017.9 or later, can you please send me the ~/.config/matplotlib/matplotlibrc file as an attachment?
So most of the plugins are 2017.12.0, and a few 2017.12.1, so later release than 2017.9 anyway.
I have entered the command you suggested in the terminal and re-run the feature-table summary command, but still got the same message.
I have looked in the matplotlibrc file but there is nothing apart from this line: “backend: Agg”, which I guess is consistent with the message: Bad key ““backend” on line 1 in /home/am14262/.config/matplotlib/matplotlibrc, as that’s the only line…
Hi @Alex_14262! I’m not exactly sure what’s going on here. Just to be sure, can you try removing the matplotlibrc file you created, run the export MPLBACKEND='Agg' command in your terminal, and rerun the feature-table command? Also, please send me the output from running echo $MPLBACKEND after running the export command above.
Also, are you running these commands directly on the server, or are they being submitted to a cluster queueing system or being run from a shell script? I wonder if the environment variables in the execution environment are different from your user environment.
I am running the commands from a shell script within my virtual box, but I am logged in on the server - this is because I have had memory issues when trying to run some of the commands directly on my laptop.
Just for clarification - any idea what the problem actually was? It may be worth mentioning that I got the Bad key message mentioned above when running all the commands in the Moving Pictures tutorial, but I still got the output - and I can't see anything wrong with the visualizations created, so I don't know if I should rerun the whole analysis. This happened only after creating the matplotlibrc file with: echo “backend: Agg” > ~/.config/matplotlib/matplotlibrc .
Since you're running the commands within a shell script on the server, it's possible that environment variable was being unset or overridden within the script (i.e. the environment variable that QIIME 2 was setting automatically for headless servers). It sounds like you have the correct configuration in place now though for the shell script's environment variables, so hopefully this won't continue to be an issue (let us know if that isn't the case).
I don't know what the exact issue was, but I suspect you had a corrupted matplotlib config file somehow, and matplotlib was upset about that. Perhaps matplotlib was just issuing a warning though, which is why the commands continued to run and produce outputs. This is just a configuration issue with matplotlib working on a headless server, so the results you obtained are reliable and won't have changed in any way based on the matplotlib error/warning. No need to rerun the analyses luckily!
Let us know if you run into any more issues. I think it was just a corrupted config file, and now that it's removed things should run smoothly.