Duplicate taxon names after merging biom tables

Hi all,

I am trying to combine two biom (and qza) tables together. The issue that is coming up is that there are several duplicate taxa rows. For instance, I get two rows with Ruminococcus torques. Does anyone have an idea what is causing this? I inputted everything into Excel and the names are duplicates which means that there is not an invisible space or difference in capitalization. I have tried to convert the biom files into txt and then into qza files. I merged the qza files and I am still getting the same result–two rows with the same feature ID. Any help will be greatly appreciated!

Hi @SterlingWright2016!

Without specific commands run and outputs observed, it is hard to say. But, at first glance, this isn't surprising to me at all, for one reason: multiple features can have the same taxonomic identification.

Duplicate feature IDs shouldn't be possible - can you please share more specific information?


Hi @thermokarst,

I was using the merge_otu_table.py in QIIME1 to combine two biom tables. An example output looked like the following

Samples Sample 1 Sample 2 Sample 3 Sample 4
Ruminococcus 0 0 5 5
Ruminococcus 5 5 0 0

I made sure that that there were no invisible characters or spaces between the rows. Excel showed that they were duplicate rows. Thus, I was very confused why the qiime command was not putting them together.
Both biom tables were exported from MEGAN5. I was never able to figure out how to solve it with QIIME. So I had to put everything in excel and then take the greatest value out of the duplicate rows. Not the most efficient way still.

Hi @SterlingWright2016 - we do not provide support for QIIME 1 on this forum - QIIME 1 was discontinued January 1st 2018 and replaced by QIIME 2. If you would like to use QIIME 2 to perform the collapsing step, please see this command:


You can see an example of its usage here:



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