Hello, I’m trying to calculate first differences for a taxa in my samples. I first exported the table.qza into feature-table.biom then converted to tsv. The first-differences command is:
qiime longitudinal first-differences --m-metadata-file test_metadata.tsv --m-metadata-file test_feature-table.transposed.edit.tsv --p-state-column week --p-metric 'D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Actinomycetales;D_4__Actinomycetaceae;D_5__Actinomyces' --p-individual-id-column SampleID --p-replicate-handling random --o-first-differences first-differences.qza
But it results in an error message:
Plugin error from longitudinal:
SampleID is not a column in your metadata
Debug info has been saved to /tmp/qiime2-q2cli-err-pt_orvhh.log
But I checked that both of my metadata files has “SampleID” in the first column. Here I copy a snippet from feature-table.transposed.edit.tsv:
SampleID | D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Actinomycetales;D_4__Actinomycetaceae;D_5__Actinomyces |
---|---|
sample-a-1 | 0.02 |
sample-a-2 | 0.04 |
sample-b-1 | 0.05 |
sample-b-2 | 0.06 |
And here I copy a snippet from metadata.tsv:
SampleID | Subject | week |
---|---|---|
sample-a-1 | sample-a | 1 |
sample-a-2 | sample-a | 2 |
sample-b-1 | sample-b | 1 |
sample-b-2 | sample-b | 2 |
I have read the tutorial at https://docs.qiime2.org/2018.2/plugins/available/longitudinal/first-differences/ and updated qiime2 to the lastest version (2018.2). I have validated both metadata files in Keemei (both the test_metadata.tsv and the real one). Please help look into this issue. Thank you!