qiime 2.2020.8 biplot plugin error

[MarcelK]

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
--i-biplot Sja-ordination.qza
--m-sample-metadata-file Map18CMR2.tsv
--m-feature-metadata-file Taxon.qza
--o-visualization biplot/Sja-biplot.qzv
--p-number-of-features 10

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.

Thanks,
Marc.

[SoilRotifer (Mike Robeson)]

Hi @MarcelK,

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 \
  --p-number-of-features 10

Also, if you copy and past sometimes the -- portion of the flags can be converted to a single long dash.

[MarcelK]

Sorry, I caught that right away. Thanks though