beta group significance

User Support
1

I was trying to the Atacama microbiome analysis with qiime2. While running the beta diversity analysis, I am getting some error messages with missing option.
The command I used for this: qiime diversity beta-group-significance \
--i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza \
--m-metadata-file sample-metadata.tsv \
--m-metadata-column transect-name \
--o-visulaization core-metrics-results/unweighted-unifrac-transect-name-significance.qzv \
--p-pairwise

The error messages I am getting :
There were some problems with the command:
(1/4) Missing option '--i-distance-matrix'.
(2/4) Missing option '--m-metadata-file'.
(3/4) Missing option '--o-visualization'. ("--output-dir" may also be used)
(4/4) Got unexpected extra arguments ( --i-distance-matrix core-metrics-
results/unweighted_unifrac_distance_matrix.qza --m-metadata-file sample-
metadata.tsv --m-metadata-column transect-name --o-visualization core-
metrics-results/unweighted-unifrac-transect-name-significance.qzv
--p-pairwise)

2 Likes
2

Welcome to the forums! :qiime2:

That's strange, because I see you are passing those options in your command:

qiime diversity beta-group-significance \
--i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza \
--m-metadata-file sample-metadata.tsv \
--m-metadata-column transect-name \
--o-visulaization core-metrics-results/unweighted-unifrac-transect-name-significance.qzv \
--p-pairwise

Are there any extra spaces after the \ slashes \ ending each line? That can confuse the Linux terminal.

Also, check the spelling!

--o-visulaization
--o-visualization

P.S. No need to post twice! We read all the posts :open_book:

3

Sorry. I corrected the spelling of visualization. But there is spaces after the slashes. This is the original one:

qiime diversity beta-group-significance \
  --i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file sample-metadata.tsv \
  --m-metadata-column body-site \
  --o-visualization core-metrics-results/unweighted-unifrac-body-site-significance.qzv \
  --p-pairwise

qiime diversity beta-group-significance \
  --i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file sample-metadata.tsv \
  --m-metadata-column subject \
  --o-visualization core-metrics-results/unweighted-unifrac-subject-group-significance.qzv \
  --p-pairwise

can you please guide me where is the fault of my command?

4

It can be hard to describe in a forum post, but ideally there will be slashes at each line except the last one, and no spaces after that. The slash shows the command it continued on the next line.

image

  1. No ending \ to show that command continues
  2. Ending slash, but extra space which confuses the terminal
  3. Perfect!

Other than that, your commands look good!

5

Thank you very much. I really appreciate it. It worked.

1 Like
6

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