feature-table error : Samples IDS is absent of the metadata ?

Technical Support
1

Hi everyone,

I’m struggling to run the following command:
qiime feature-table summarize --i-table table.qza --o-visualization table.qzv --m-sample-metadata-file whole_16s_ktbiome_1-2-3-4-5.tsv.tsv

Because I get the following error message:
Plugin error from feature-table:

The following IDs are not present in the metadata: 'KTBIOME385', 'KTBIOME386', 'KTBIOME387', 'KTBIOME388', 'KTBIOME389', 'KTBIOME390', 'KTBIOME391', 'KTBIOME392', 'KTBIOME393', 'KTBIOME394', 'KTBIOME395', 'KTBIOME396', 'KTBIOME397', 'KTBIOME398', 'KTBIOME399', 'KTBIOME400', 'KTBIOME401', 'KTBIOME402', 'KTBIOME403', 'KTBIOME404', 'KTBIOME405', 'KTBIOME406', 'KTBIOME407', 'KTBIOME408', 'KTBIOME409', 'KTBIOME410', 'KTBIOME411', 'KTBIOME412', 'KTBIOME413', 'KTBIOME414', 'KTBIOME415', 'KTBIOME416', 'KTBIOME417', 'KTBIOME418', 'KTBIOME419', 'KTBIOME420', 'KTBIOME421', 'KTBIOME422', 'KTBIOME423', 'KTBIOME424', 'KTBIOME425', 'KTBIOME426', 'KTBIOME427', 'KTBIOME428', 'KTBIOME429', 'KTBIOME430', 'KTBIOME431', 'KTBIOME432', 'KTBIOME433', 'KTBIOME434', 'KTBIOME435', 'KTBIOME436', 'KTBIOME437', 'KTBIOME438', 'KTBIOME439', 'KTBIOME440', 'KTBIOME441', 'KTBIOME442', 'KTBIOME443', 'KTBIOME444', 'KTBIOME445', 'KTBIOME446', 'KTBIOME447', 'KTBIOME451', 'KTBIOME452', 'KTBIOME453', 'KTBIOME454', 'KTBIOME455', 'KTBIOME456', 'KTBIOME457', 'KTBIOME458', 'KTBIOME459', 'KTBIOME460', 'KTBIOME461', 'KTBIOME462', 'KTBIOME463', 'KTBIOME464', 'KTBIOME465', 'KTBIOME466', 'KTBIOME467', 'KTBIOME468', 'KTBIOME469', 'KTBIOME470', 'KTBIOME471', 'KTBIOME472', 'KTBIOME473', 'KTBIOME474', 'KTBIOME475', 'KTBIOME476', 'KTBIOME477', 'KTBIOME478', 'KTBIOME479', 'KTBIOME480'

Debug info has been saved to tmp/qiime2-q2cli-err-xuzbj6ol.log

Apparently, there are some missing samples.
I checked the metadata file. The spelling seems to be ok.
I verified the metadata formatting using Keimei, everything is OK.
I have ran feature-table without the --m-sample-metadata-file, and then I visualized the table.qzv, those samples are in the list.
Here attached the table.qza and the metadata file table.qza (95.1 KB) whole_16s_ktbiome_1-2-3-4-5.tsv (24.3 KB)

Any idea, suggestions?
Thanks in advance
Maxime

3

Hi @Eolden,

Welcome to the :qiime2: forum!

Could you please try summarizing your feature table without the metadata so you can see what features. are present?

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

Best,
Justine

PS You can make your code easier to read with the ` character. On an english keyboard, it usually lives with the ~ key.

4

Dear Justine,
Thanks to your help, I verified that the metadata are complete.
The work is not working for now…
Thanks for your help.
Best
Maxime

5

Hi @Eolden,

Have you verified the IDs in your table? Your metadata may be complete, but if there’s somehow a mismatch between IDs (spaces can get you), your metadata may be correct but that doesn’t mean it matches your feature table.

Best,
Justine

6

Dear Justine @jwdebelius ,
I verified my IDs.
But I finally find the problem.
I don’t know the reason why but the metadata was in wrong coding (LF versus CRF). I modified it using Notepad ++ and it finally succed to run the pipeline.
Thanks for your valuable help!
Maxime

2 Likes
7

Hi @Eolden,

I’m glad you solved it. That was not at all what I was expecting; thank you for teaching me something new!

Best,
Justine

1 Like
8

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