I’m following the tutorial for the longitudinal workflow. I am running QIIME2 v. 2018.11. I successfully used the feature-volatility script on a collapsed taxa file to produce a volatility plot of important features using this command:
qiime longitudinal feature-volatility \ --i-table collapsed_table_lev-6.qza \ --m-metadata-file mapping_cessation.txt \ --p-state-column days_on_risp \ --p-individual-id-column Mouse_num \ --p-n-estimators 80 \ --p-random-state 123 \ --output-dir longitudinal/taxa_volatility_RF_80_est
I found a few taxa that look like they could be interesting for further analysis. I saw in the tutorial that you can look at specific features using LME:
Its average frequency is greater in vaginally born subjects than cesarean-delivered subjects, so could be an interesting candidate for statistical testing, e.g., with
When I tried to do this I ran into problems. I would appreciate any help in figuring out what I’m doing wrong. To be clear, I’m trying to use an important feature from the feature-volatility command in the LME statistical model. This is the command I tried:
qiime longitudinal linear-mixed-effects \ --m-metadata-file mapping_cessation.txt \ --m-metadata-file longitudinal/taxa_volatility_RF_80_est/feature_importance.qza \ --p-metric k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Oscillospira \ --p-state-column days_on_risp \ --p-individual-id-column Mouse_num \ --p-group-columns treat_group \ --o-visualization longitudinal/vis_LME_Oscillospira.qzv
This gave me an error:
"Cannot merge because there are no IDs shared across metadata "
ValueError: Cannot merge because there are no IDs shared across metadata objects.
-bash: p__Firmicutes: command not found
-bash: c__Clostridia: command not found
-bash: o__Clostridiales: command not found
-bash: f__Ruminococcaceae: command not found
-bash: g__Oscillospira: command not found
I chose that metric by using the TSV file from the Volatility Control Chart and looking at the column titles (the important features I’m interested in). There are values for each sample in that column.
Any help you can give would be great!