Hello everyone,
I was able to generate PERMANOVA p-value for weighted UniFrac for "diseasextimexHTNo" column. But when I used this same code to generate p-value for "diseasextimexHTYes" column, I ran into issue below. Was it because of "MBP" thing appeear after my name ( (base) hando@Cinderellas-MBP). What is MBP and what is it used for?
Thank you so much for your help!
(base) hando@Cinderellas-MBP ~ % conda activate qiime2-2023.5
(qiime2-2023.5) hando@Cinderellas-MBP ~ % cd /Users/hando/Desktop/AlphaDiversity_FS
(qiime2-2023.5) hando@Cinderellas-MBP AlphaDiversity_FS % list
zsh: command not found: list
(qiime2-2023.5) hando@Cinderellas-MBP AlphaDiversity_FS % ls
Data.pptx meta_FS_sexpartners.tsv
core-metrics-results meta_FS_sexpartners.xlsx
core-metrics-results1 metadata.tsv
core-metrics-results2 metadata1.tsv
core-metrics-results3 metadata1.xlsx
core-metrics-results4 metadata2.tsv
core-metrics-results7 metadata2.xlsx
core-metrics-results8 metadata4.tsv
faith-pd-group-significance1.qzv metadata4FS.xlsx
faith_pd_vector.qza metadata7.tsv
filtered-feature-table.qza metadata8.xlsx
meta_FS1.tsv metadata9.tsv
meta_FS1.xlsx rooted_tree.qza
(qiime2-2023.5) hando@Cinderellas-MBP AlphaDiversity_FS % qiime diversity beta-group-significance
--i-distance-matrix core-metrics-results8/weighted_unifrac_distance_matrix.qza
--m-metadata-file meta_FS1.tsv \
--m-metadata-column diseasextimexHTNo \
--o-visualization core-metrics-results8/weighted-unifrac-diseasextimexHTNo-significance.qzv
--p-pairwise
Saved Visualization to: core-metrics-results8/weighted-unifrac-diseasextimexHTNo-significance.qzv
(qiime2-2023.5) hando@Cinderellas-MBP AlphaDiversity_FS % qiime diversity beta-group-significance
--i-distance-matrix core-metrics-results8/weighted_unifrac_distance_matrix.qza
--m-metadata-file meta_FS1.tsv
--m-metadata-column diseasextimexHTYes \
--o-visualization core-metrics-results8/weighted-unifrac-diseasextimexHTYes-significance.qzv
--p-pairwise
Usage: qiime diversity beta-group-significance [OPTIONS]
Determine whether groups of samples are significantly different from one
another using a permutation-based statistical test.
Inputs:
--i-distance-matrix ARTIFACT
DistanceMatrix Matrix of distances between pairs of samples.
[required]
Parameters:
--m-metadata-file METADATA
--m-metadata-column COLUMN MetadataColumn[Categorical]
Categorical sample metadata column. [required]
--p-method TEXT Choices('permanova', 'anosim', 'permdisp')
The group significance test to be applied.
[default: 'permanova']
--p-pairwise / --p-no-pairwise
Perform pairwise tests between all pairs of groups in
addition to the test across all groups. This can be
very slow if there are a lot of groups in the metadata
column. [default: False]
--p-permutations INTEGER
The number of permutations to be run when computing
p-values. [default: 999]
Outputs:
--o-visualization VISUALIZATION
[required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr during
execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
There were some problems with the command:
(1/3) Missing option '--m-metadata-file'.
(2/3) Missing option '--o-visualization'. ("--output-dir" may also be used)
(3/3) Got unexpected extra argument ( )
zsh: command not found: --m-metadata-column
zsh: command not found: --o-visualization