Any updates on the ignore_missing_samples argument for core_diversity? It´s driving me crazy to have to select my samples manually
Keep up the good work!
That flag was added to the visualizers in q2-emperor in the 2018.11 release!
Thanks! Sounds awesome! Just updated to qiime2-2018.11 in conda and tried:
qiime diversity core-metrics-phylogenetic --i-table filtered-table_f4s3.qza --i-phylogeny fasttree_rooted.qza --p-sampling-depth 9272 --m-metadata-file short_meta_full_names.txt --p-n-jobs 2 --output-dir core_div_phylo_9272/ --verbose --p-ignore-missing-samples
Usage: qiime diversity core-metrics-phylogenetic [OPTIONS]
Try “qiime diversity core-metrics-phylogenetic --help” for help.
Error: no such option: --p-ignore-missing-samples
Can you see what´s wrong?
Yep! I wasn’t as clear as I should’ve been in my initial reply:
ignore_missing_samples flag have been added to:
The param can be used by directly running one of those q2-emperor commands directly. That parameter has not been exposed in the
diversity core-metrics or
diversity core-metrics-phylogenetic pipelines, and I don’t think we are currently planning on making that change, since it is so specific to q2-emperor. If you want to take advantage of that new parameter, you can run the constituent commands on their own, remembering to supply the
ignore_missing_samples flag as appropriate. Since you are asking about emperor specifically, you can skip all of the alpha steps and skip straight to the beta metrics.
See the flowchart here for a list of the constituent commands.
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