I’m trying to run
qiime longitudinal volatility with feature relative frequency as the metric. I can’t figure out what artifact column to use. In fact, I’m not entirely sure how to view the column names of feature table artifacts.
p-metric Frequency would be the appropriate column name but it won’t work. I’ve tried various combinations of feature, relative, and frequency.
> qiime longitudinal volatility \
> --m-metadata-file GenBMT-metadata-complete.tsv \
> --p-group-column RoomType \
> --p-metric Frequency \
> --p-state-column SamplingIntervalCode \
> --p-individual-id-column Patient \
> --i-table environmental-samples/table-relative-frequencies-environmental-samples-contaminant-free-feature-filtered.qza \
> --p-ci 95 \
> --p-plot-control-limits \
> --o-visualization environmental-samples/volatility-feature-RoomType.qzv
The error message is always:
Plugin error from longitudinal:
metric must be a valid metadata or feature table column.
Debug info has been saved to /tmp/qiime2-q2cli-err-31175805.log
I’m sure there is an easy solution here…
In this case,
metric should be a specific feature name (e.g., taxon or sequence variant ID).
tabulate-seqs (example here) to get a summary of the feature names; otherwise, if you’ve collapsed to taxonomy, use the name of a taxon of interest.
I hope that clarifies this action for you!
Thanks for the reply @Nicholas_Bokulich.
I’ve got this command to work using specific feature names for
metric, but not with taxa names. By collapsing to phylum level, I get taxa labels like “D_0__Bacteria;D_1__Actinobacteria.”
qiime longitudinal volatility doesn’t seem to work with “D_0__Bacteria;D_1__Actinobacteria” as the metric. Maybe the semi-colon is throwing it off?
Error: Missing option: --p-state-column
Error: Missing option: --p-individual-id-column
Error: Missing option: --o-visualization
Note: When only providing names for a subset of the output Artifacts or
Visualizations, you must specify an output directory through use of the
--output-dir DIRECTORY flag.
-bash: D_1__Actinobacteria: command not found
I believe you are correct — the semicolon causes the error because
; is a LINUX/UNIX special character that is being interpreted by the shell. You should enclose the entire taxon name in single quotes to prevent that issue. Could you please let me know if that works and if not please provide the exact command that got that error message.
Yup, I was missing single quotes. It works perfectly now.
awesome — thanks for reporting back!
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.