BIOMV100Format rejected when trying to import .biom file from QIIME v. 1.9.1

[dgoldsmith]

Using the tutorial for importing QIIME 1 output files into QIIME 2 (version 2018.6), I am running the following command:

qiime tools import --input-path otu_table_mcl.biom --type ‘FeatureTable[Frequency]’ --source-format BIOMV100Format --output-path otu_table_mc1.qza

In response, I get the following error:

[thermokarst]

Hey there @dgoldsmith, looks like your error log didn’t get attached!

[dgoldsmith]

Yes, I hit “send” (or “create”) too soon. I just submitted a complete topic now. Thanks for quick reply.

[dgoldsmith]

Following the 2018.6 tutorial for importing data, I am trying to import a .biom table created in QIIME v 1.9.1 for use in QIIME 2 (for alpha and beta diversity analyses). I’m using the following command:

qiime tools import --input-path otu_table_mcl.biom --type ‘FeatureTable[Frequency]’ --source-format BIOMV100Format --output-path otu_table_mc1.qza

When I run that command, I get the following response:

There was a problem importing otu_table_mcl.biom:

otu_table_mcl.biom is not a(n) BIOMV100Format file

The table I’m trying to import was produced by a colleague using QIIME 1.9.1. I tried changing the format type to BIOMV190Format and BIOMV191Format (in case those exist as proper arguments for the command), but that didn’t work.

If the file I’m passing to QIIME is not in BIOMV100Format, how can I figure out what format it’s actually in, and then how can I import it for conversion to .qza and use in QIIME 2?

Thank you.

[colinbrislawn (Colin J Brislawn)]

Good afternoon,

I think you are on the right track!

I tried changing the format type to BIOMV190Format and BIOMV191Format

Qiime 1.9.1 outputs .biom files in the BIOMV210Format. Strange, right? It turns out that biom versions and qiime version are unrelated.

Try that same command again using
--source-format BIOMV210Format
and let us know if that works.

Colin

[dgoldsmith]

Colin,
That works perfectly. Thank you immensely!

–Dawn