I am new to both bioinformatics and Qiime entirely, i was able to run the moving picture turtorial successfully. now working arounf my data, running the following command
qiime diversity beta-group-significance --i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza --m-metadata-file inoculum2-sample-metadata.tsv --m-metadata-column sampleid --o-visualization core-metrics-results/unweighted-unifrac-body-site-significance.qzv --p-pairwise
gives this error ( (1/1) Invalid value for '--m-metadata-file': There was an issue with
retrieving column 'sampleid' from the metadata.).
i read up other issues in the forum but couldnt still get it, although i changed to a different colunm (Sample-number-or-well-position) after reading several issues then came up with a different error (Plugin error from diversity:
All values in the grouping vector are unique. This method cannot operate on a grouping vector with only unique values (e.g., there are no 'within' distances because each group of objects contains only a single object).
Debug info has been saved to /tmp/qiime2-q2cli-err-gqt1ixaz.log). Attached is my metadata sample-metadata.tsv (4.1 KB)
Thank you.
Hi @pyghost,
Welcome to the forum!
As the error message is indicating, the column you are providing in your --m-metadata-column parameter only has unique values, meaning you are asking the diversity plugin to perform a group wise test but you are providing no groupings. I had a quick look in your metadata file and I don't really see any experimental columns that would test a hypothesis. You'll want to provide a column that has some grouping memberships, for example a treatment, a group, a phenotype etc.
Hi!
Welcome to the forum!
The error you are facing occurs when one provides a column with all unique values as metadata column to perform statistical analysis. You need to provide a column with non-unique (but at least with 2 groups) values, so the plugin could group all samples in the dataset according to column values and perform stat. analysis between groups.