Feature-table summarize metadata index problem

[Alex_14262 (Alexandru Mandrut)]

Thanks @Micro_Biologist!

I successfully created the interactive quality plot, chose the parameters for DADA2, and ran the script.

However, when I tried to create the visual summaries of the data with the command:

qiime feature-table summarize \

--i-table table-dada2.qza
--o-visualization table.qzv
--m-sample-metadata-file qiime_map2.tsv

I got this error and I am not sure how to fix it:

Plugin error from feature-table:

"None of [Index(['ACTGCTGA', 'CAGTGACT', 'CTGACTGA', 'TCAGAGTC', 'CAGTCTGA', 'ACTGCAGT',\n 'AGTCCAGT', 'CAGTCAGT', 'CAGTGTCA', 'CTGAACTG', 'ACTGACTG', 'CTGAGACT',\n 'AGTCGTCA', 'AGTCGACT', 'AGTCACTG', 'CTGAAGTC', 'ACTGAGTC'],\n dtype='object')] are in the [index]"

Debug info has been saved to /tmp/qiime2-q2cli-err-nxqtwh6r.log

This is the metadata file I am using:

qiime_map2.tsv (1.2 KB)

[jairideout (Jai Ram Rideout)]

Hi @Alex_14262! It looks like none of the sample IDs in your metadata file are contained in the feature table (table-dada2.qza). Can you try inspecting the sample IDs that are present in your feature table, and compare those to the sample IDs in the metadata file?

To see what sample IDs are in the feature table (among other things), you can run the feature-table summarize command without metadata:

qiime feature-table summarize \
--i-table table-dada2.qza 
--o-visualization table.qzv 

Thanks!

[Alex_14262 (Alexandru Mandrut)]

Hi @jairideout, thanks for the help! I managed to fix it. The barcodes in the mapping file contained a number at the end of the sequence which caused the error for some reason.

On that note, what is the difference between running the feature-table summarize with and without the metadata? I didn’t find a difference apart from the graph under the “interactive sample detail” tab which was missing when I didn’t include the metadata.

[jairideout (Jai Ram Rideout)]

Hi @Alex_14262, glad you were able to resolve the sample ID / barcodes issue!

@Alex_14262

On that note, what is the difference between running the feature-table summarize with and without the metadata? I didn’t find a difference apart from the graph under the “interactive sample detail” tab which was missing when I didn’t include the metadata.

That's the only difference!