longitudinal pairwise-differences artifacts

User Support
1

Hi everyone,
I am running the QIIME2 FMT tutorial. Now trying to answer the questions on the longitudinal aspect of the FMT tutorial, under diversity analysis.
I ran the following and obtained an error message:

$ qiime longitudinal pairwise-differences
--m-metadata-file sample-metadata.tsv
--m-metadata-file core-metrics-results/shannon_vector.qza
--p-metric shannon
--p-group-column treatment-group
--p-state-column week
--p-state-1 0
--p-state-2 18
--p-individual-id-column subject-id
--p-replicate-handling random
--o-visualization pairwise-differences.qzv

Plugin error from longitudinal:
metric must be a valid metadata or feature table column.
Debug info has been saved to /var/folders/sv/fhp_w8c10p9dgwz2jlkdvw7rjl9c9d/T/qiime2-q2cli-err-oj262apn.log

What FeatureTable should I use to complete this plugin? How can I explore what the FeatureTable[Frequency] or the FeatureTable[Sequence] contain in a human readable format?
What is the difference between the table.qza and any of the tables created in the core-metrics folder after running the core-metrics plugin? Which one should be used to measure any of the diversities?
thanks a lot!

2

Hi!
If you are using the latest Qiime2 release, provide shannon_entropy instead of shannon as a metric

3 Likes
3

@timanix Thanks for your answer. I performed the change and received this error:

$ qiime longitudinal pairwise-differences
--m-metadata-file sample-metadata.tsv
--m-metadata-file core-metrics-results/shannon_vector.qza
--p-metric shannon_entropy
--p-group-column treatment-group
--p-state-column week
--p-state-1 0
--p-state-2 18
--p-individual-id-column subject-id
--p-replicate-handling random
--o-visualization pairwise-differences.qzv

Plugin error from longitudinal:
State 0.0 is not represented by any members of donor group in metadata. Consider using a different group_column or state value.
Debug info has been saved to /var/folders/sv/fhp_w8c10p9dgwz2jlkdvw7rjl9c9d/T/qiime2-q2cli-err-0v82fq33.log

4

This error is self-explanatory - looks that state 1 "0" is not represented for some group in your metadata. You need to choose another state or add missing samples to your analysis

2 Likes
5

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