Dear all,
I am trying to running the qiime diversity alpha-rarefaction command, which is according to the Moving pictures tutorial, but met with this problem. Could you please help?
iime2-amplicon-2023.9) yiggrite@MWMJ07RHBF:~/ClaraA16s$ qiime diversity alpha-rarefaction \
--i-table table2.qza
--i-phylogeny rooted-tree2.qza
--p-max-depth 47000
etadata-file metadata-file2.tsv
--o-visualization core-metrics-results2-3/alpha-rarefaction2-3.qzv
Usage: qiime diversity alpha-rarefaction [OPTIONS]
Generate interactive alpha rarefaction curves by computing rarefactions
between min_depth and max_depth. The number of intermediate depths to
compute is controlled by the steps parameter, with n iterations being
computed at each rarefaction depth. If sample metadata is provided, samples
may be grouped based on distinct values within a metadata column.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency]
Feature table to compute rarefaction curves from.
[required]
--i-phylogeny ARTIFACT Optional phylogeny for phylogenetic metrics.
Phylogeny[Rooted] [optional]
Parameters:
--p-max-depth INTEGER The maximum rarefaction depth. Must be greater than
Range(1, None) min-depth. [required]
--p-metrics TEXT... Choices('ace', 'berger_parker_d', 'brillouin_d',
'chao1', 'dominance', 'doubles', 'enspie', 'faith_pd', 'fisher_alpha',
'gini_index', 'goods_coverage', 'heip_e', 'lladser_pe', 'margalef',
'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit',
'observed_features', 'pielou_e', 'robbins', 'shannon', 'simpson',
'simpson_e', 'singles')
The metrics to be measured. By default computes
observed_features, shannon, and if phylogeny is
provided, faith_pd. [optional]
--m-metadata-file METADATA...
(multiple arguments The sample metadata.
will be merged) [optional]
--p-min-depth INTEGER The minimum rarefaction depth.
Range(1, None) [default: 1]
--p-steps INTEGER The number of rarefaction depths to include between
Range(2, None) min-depth and max-depth. [default: 10]
--p-iterations INTEGER The number of rarefied feature tables to compute at
Range(1, None) each step. [default: 10]
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:
(1/2) Missing option '--o-visualization'. ("--output-dir" may also be used)
(2/2) Got unexpected extra argument ( )
(qiime2-amplicon-2023.9) yiggrite@MWMJ07RHBF:~/ClaraA16s$ --m-metadata-file metadata-file2.tsv
--m-metadata-file: command not found
(qiime2-amplicon-2023.9) yiggrite@MWMJ07RHBF:~/ClaraA16s$ --o-visualization core-metrics-results2-3/alpha-rarefaction2-3.qzv
--o-visualization: command not found
(qiime2-amplicon-2023.9) yiggrite@MWMJ07RHBF:~/ClaraA16s$
