I am running Qiime 2 2020.8 on a cluster. I am using the
qiime emperor biplot plugin to obtain biplot visualization. I chose to display 10 features.
qiime emperor biplot
The indicates this :Saved Saved Visualization to: biplot/Sja-biplot.qzv
/tmp/slurmd/job61850073/slurm_script: line 22: --p-number-of-features: command not found
Please let me know if there is anything I can do from our end.
It’d be more helpful to see the actual slurm batch script file. I’d suspect that you are missing a
\ at the end of one of the lines. This tells the shell that your command is spread out over multiple lines.
Your command should look something like this:
qiime emperor biplot \
--i-biplot Sja-ordination.qza \
--m-sample-metadata-file Map18CMR2.tsv \
--m-feature-metadata-file Taxon.qza \
--o-visualization biplot/Sja-biplot.qzv \
Also, if you copy and past sometimes the
-- portion of the flags can be converted to a single long dash.
Sorry, I caught that right away. Thanks though
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