Decontam Issues with importing taxonomy table

I am trying to use Decontam to clean my data. This is my first time using it and I am running into an issue with my taxonomy table. When uploading my taxa table and taxonomy into R I am using the following script and this is working find:

physeq<-qza_to_phyloseq(features="table_lily2.qza", taxonomy="Aphaenogaster_taxonomy.qza")

However the taxa count is only 4 in my OTU table and I get this result:

phyloseq-class experiment-level object
otu_table() OTU Table: [ 4 taxa and 59 samples ]
tax_table() Taxonomy Table: [ 4 taxa by 7 taxonomic ranks ]

The issue is that when I use the exact same table_lily2.qza to create a bar plot I can clearly see that there are way more than 4 taxa, so I do not know what the issue is. I tried to look up why this may be happening but I am not finding any resources.

Hi @liliez13 I am unsure about why your taxonomies are different, but from my understanding you are trying to upload a qiime obj into R as a phyloseq obj to use Decontam correct? If so you can sidestep this by using the latest Qiime distribution to run Decontam processes as the functionality is integrated into the quality-control plugin

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I only have two controls so I am unable to use the qiime distributionto run Decontam since it requires a minimum of 5 control samples.
Do you have another suggestion on why this may be occuring?

Ah I see, it was initially implemented in that way as the recommended number of control samples is 5, however in later distributions this requirement was removed, in favor of a warning message. Which Qiime distribution are you using?

You see more info about control requirements for decontam here.

I am using Qiime2-2023.5

That is the first distribution of Qiime to use decontam so it has the initial implementation that has the requirement of 5 control samples. All you have to do is upgrade your qiime2 distribution to the latest and you shouldn't have a problem!

You can do that here

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