Error de Qiime2 Empress

Community Plugin Support
1

Hi Everyone,

I’m working in qiime2-2021.2.0 and I have this error message when i ran this:

qiime empress community-plot
--i-tree Documentos/q2_mundo/hs_sed_tree.qza
--i-feature-table Documentos/q2_mundo/archivos_qza/hs_sed_table.qza
--m-sample-metadata-file Documentos/q2_mundo/hs_sed_table.tsv
--m-feature-metadata-file Documentos/q2_mundo/archivos_qza/hs_sed_taxonomy.qza --o-visualization hs_sed_community_tree-viz.qzv

Plugin error from empress:

No samples in the feature table are present in the sample metadata.

Debug info has been saved to /tmp/qiime2-q2cli-err-gp5wjp8v.log

However, when I review my files they are fine. I put the files in conflict. I would appreciate any help

hs_sed_table.qzv (4.1 MB)

hs_sed.tsv (6.5 KB)

2

Hi,

Thanks for using Empress! The sample metadata file you have provided (hs_sed.tsv) looks fine, as far as I can tell. However, the table you've provided is a QZV (a QIIME 2 visualization) instead of a QZA (a QIIME 2 artifact) -- in order to help with debugging, could you please provide the hs_sed_table.qza file referenced in your command? If you could also provide the tree and taxonomy files used, hs_sed_tree.qza and hs_sed_taxonomy.qza, that would be useful.

From what I can tell: the table visualization you have provided uses sample IDs that match up perfectly with your sample metadata file. So I am not sure what the problem is yet. It will help to look at the other QZAs; something strange might be happening with the filtering process in Empress.

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3

Hi @fedarko

Thanks a lot for your response. Sure I put the files:

hs_sed_taxonomy.qza (3.5 MB)

hs_sed_table.qza (3.2 MB)

I can't upload my tree file because it is too big.

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4

Hi @fellora,

Thanks for sending the files. I've checked them out, and as far as I can tell they seem perfect! The taxonomy's features match perfectly with the table's features, and the table's samples match perfectly with the sample metadata's samples.

However, reading through things again, I think I might have discovered the reason you were getting an error. The command you posted in your first comment above includes the following line:

--m-sample-metadata-file Documentos/q2_mundo/hs_sed_table.tsv

I suspect that hs_sed_table.tsv is the wrong file to use here. Since your command did not trigger an error about this file not existing, we can conclude it exists :slight_smile: I'm guessing that this is not your sample metadata file, but is instead a TSV (tab-separated values) representation of your feature table.

If this is the case, this explains why you got the "No samples in the feature table are present in the sample metadata" error: BIOM tables stored in TSV format usually have features as the row indices instead of samples, so Empress is interpreting hs_sed_table.tsv as a sample metadata file where all the "sample IDs" are really feature IDs (e.g. "00009a156f31023e7f5fd003fec55c99", "00012f2bd18bd48d27a5656f65afe71d", etc.)

Long story short, I think you should be able to fix this command and get Empress working if you change the --m-sample-metadata-file parameter to point to

--m-sample-metadata-file Documentos/q2_mundo/hs_sed.tsv

...or wherever your sample metadata file is located.

Let me know if this fixes things! If not, we can troubleshoot further.

1 Like
5

Hi @fedarko

You are fine. It was a writing mistake! it works know!! Thank to you for such an amazing plugin!!

1 Like