qiime2.core.exceptions.ValidationError: Missing one or more files for BIOMV210DirFmt: 'feature-table.biom'

Technical Support
1

Dear all
I am a new user and this bug bother me two days
When i use
qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table.qza
--p-sampling-depth 50000
--m-metadata-file metadata.tsv
--output-dir core-metrics-results
I get the error:
qiime2.core.exceptions.ValidationError: Missing one or more files for BIOMV210DirFmt: 'feature-table.biom'
I dont know what it means, and i tried these code to solve it:
qiime tools export --input-path table.qza --output-path exported-feature-table
qiime tools export --input-path taxonomy.qza --output-path exported-feature-table
biom add-metadata -i feature-table.biom -o table-with-taxonomy.biom --observation-metadata-fp taxonomy.tsv --sc-separated taxonomy
qiime tools import --type 'FeatureTable[Frequency]' --input-path table-with-taxonomy.biom --output-path table_wtih_taxonomy.qza
Then i replace "table.qza" with "table_wtih_taxonomy.qza", it also doesnot work
I have no idea about the input file of "diversity core-metrics-phylogenetic" is just table.qza but still needs feature-table.biom

1 Like
2

Hey @ming_feng,

Welcome to the :qiime2: forum! :wave:

Essentially, this error means that the underlying feature-table.biom file appears to be missing from your input feature table (i.e. table.qza).

Would you mind sharing your table.qza with me (in a DM is fine if you'd prefer not to share publicly)? I can take a look at it and see if anything looks amiss within the zipped artifact.

Cheers :lizard:

3

table.qza (19.5 KB)
Thank you very much, here is the file

1 Like
4

Hey @ming_feng,

Thanks for sharing your table - nothing stands out as suspicious to me upon inspection. Your file is valid, a FeatureTable[Frequency] with the correct directory format, and the provenance doesn't show anything weird.

Would you mind sharing the rest of your input files, and I'll try to reproduce the error on my end? Thanks! :lizard:

5

OK，thank you very much, here are the rest of the files:
rep-seqs.qza (25.6 KB)
rooted-tree.qza (39.0 KB)
demux-summary.qzv (318.9 KB)
taxonomy.qzv (1.2 MB)

7

Hi @ming_feng,

Thanks! I'll also need your metadata file (which again you're welcome to send via DM if you don't want to share that publicly).

Cheers :lizard:

9

metadata.tsv (45 Bytes）here is the metadata file, thank you

10

Hi @ming_feng,

Thanks for sharing that file!

I ran the exact command you shared above with all of the input files you provided (rooted-tree, table, and metadata) and it ran successfully. I'm wondering if it's possible you unintentionally used a different table in your command (via shared filename in a different directory location).

Let's have you try the following:

  1. Place your rooted-tree, table, and metadata files in a specific directory (i.e. diversity-analysis or something you'll remember).
  2. Make sure you are then sitting inside of that directory before re-running the same command you shared above.

If you still receive the same error, can you provide the outputs of running the following commands:

conda list

qiime info

Thanks! :lizard: