Import paired-end demultiplexed Illumina MiSeq (2x300) data

[Gidodo (Gideon A)]

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

2. Visualize

qiime demux summarize --i-data /my/raw/data_directory/qiimed/my-paired-end.qza --o-visualization /my/raw/data_directory/qiimed/my-demux.qzv

[thermokarst]

Hey there @Gidodo!

What version of QIIME 2 are you running?

A nice summary of why you are seeing that error can be found here:

Feature table summarize Invalid DISPLAY variable

Hi @mc92! 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 or Agg, you could try running the following:

echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc 

If it does say agg or Agg, I think you will need to talk to your sysadmin and learn more about the execution environment's configuration.

Hope that helps!

[Gidodo (Gideon A)]

Thank you for your response. I am running the analysis on a Cluster environment. The current version is qiime2/2018.4.

[thermokarst]

@Gidodo

2018.4

Cool, so it isn't super old!

I will wait to hear back on the other info I requested above - thanks!