Importing .biom v 2.1.15 table into QIIME

Technical Support
1

Hi everyone,

I've spliced together taxonomy data at the family level from 10 different samples into a .tsv frequency table and converted that .tsv file into a .biom file using the command:

biom convert -i beta-diversity-table.tsv -o beta-diversity-table.biom --table-type='OTU table' --to-json

Now I'm attempting to import the .biom table into QIIME using the following command:

qiime tools import --input-path beta-diversity-table.biom --type 'FeatureTable[Frequency]' --input-format BIOMV210Format  --output-path beta-diversity-feature-table.qza

When I run the command above, I receive the following error:

There was a problem importing beta-diversity-table.biom:

  beta-diversity-table.biom is not a(n) BIOMV210Format file

I've used biom -h to sort out that I have biom v 2.1.15 installed. Do I need to use a different type for the --input-format? If so, what type? Or is there a way to write the .biom v2.1.15 table to v2.1? I would really appreciate any guidance.

2

Hello @Aaron_Bivins,

Can you please run biom convertwith --to-hdf5 not --to-json. I believe the only format of biom table we support for importing is hdf5. I apologize for the inconvenience.

3 Likes
3

Hi @Oddant1. I've done exactly as you suggested '''-to-hdf5""" and then I was able to import with BIOMW210Format.

Thank you for the help!

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