Hi! I am having an issue with the feature-table group command in Qiime2 (ver. 2017.12). Specifically, I have two sequencing runs that I am trying to merge, summing adding the OTU counts for some re-sequenced samples from run #2 using the indexes from run #1. I have successfully merged the two table.qza, ref-seqs.qza, and mapping files, and I have created a new column in the mapping file that identifies each sample by its proper index from run #1.
Then I execute the following command:
qiime feature-table group \ --i-table merged-table.qza \ --p-axis sample \ --m-metadata-file merged-map.txt \ --m-metadata-category "run1_id" \ --p-mode sum \ --o-grouped-table grouped-table.qza \
This command, while not killed, does not finish in 2 hours on a compute node with 16g of memory (which seems entirely sufficient). Do you have any idea what could be going wrong?