I am trying to do the alpha-rarefaction step and encountered an error. I will briefly explain what I did as follows.
I did the DADA2 denoising to obtain the table.qza and rep-seq.qza files. I did the taxonomy assignment using the Silva database and also I did the filtering for the mitochondria, chloroplast, and unassigned reads. After the filtering step, I reviewed the table.qzv file to check the sampling depth. When I check the sample ID and sequence count table, I found that the last two samples have low sequence counts (from the bottom: 8043, and 8085). The third sample from the bottom of this table has a 10,157 sequence count. So, I selected the sampling depth as 8086 in my analysis.
After that, I used following command for the alpha-rarefaction:
qiime diversity alpha-rarefaction
However, I had the following error:
All metadata filtered after dropping columns that contained non-categorical data.
I could not figure out this error to proceed with the analysis. So, I truly appreciate it if you could give me a possible solution for this error.
Thanks in advance!