I have some paired-end demultiplexed Illumina MiSeq (2x300) data that I want to import into QIIME 2. The import was successful, generating my-paired-end.qza, and using code # 1 below. Visualizing the data using code # 2 threw up this error message:
Plugin error from demux:
Invalid DISPLAY variable
Debug info has been saved to /scratch/local/21816035/qiime2-q2cli-err-lpp65164.log
Please is there any fix?
1. Data import
qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path /my/raw/data_directory/mydata/ --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path /my/raw/data_directory/qiimed/my-paired-end.qza
qiime demux summarize --i-data /my/raw/data_directory/qiimed/my-paired-end.qza --o-visualization /my/raw/data_directory/qiimed/my-demux.qzv
What version of QIIME 2 are you running?
A nice summary of
why you are seeing that error can be found here:
matplotlib isn’t a QIIME 2 plugin so it won’t show up in qiime info. matplotlib is a Python library for producing plots, and several QIIME 2 plugins use it internally for plotting. Since you’re getting an Invalid DISPLAY variable error from matplotlib, that means it is installed!
There’s a few posts on the forum describing how to fix this particular issue. Can you try the suggestions in this post?
QIIME 2 has been shipping with config to prevent that issue from happening, but it sounds like one of the following is impacting you:
you are running a super old version of qiime
your execution environment is preventing our config from being applied
your execution environment is overriding our config
When you run
echo $MPLBACKEND what do you see? If it doesn’t say
Agg, you could try running the following:
echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
Agg, I think you will need to talk to your sysadmin and learn more about the execution environment’s configuration.
Hope that helps!
Thank you for your response. I am running the analysis on a Cluster environment. The current version is qiime2/
Cool, so it isn’t super old!
I will wait to hear back on the other info I requested above - thanks!
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