Regarding running cluster-feature-closed-reference

Hello All
Hope you all are doing well.
I am trying hard to go through the tutorial and QIIME2forum to troubleshoot my errors.
By reaching up to otu clustering and running the closed otu command
qiime vsearch cluster-feature-closed-reference --i-table table.qza --i-sequences rep.seq.qza --i-reference-sequences 99_otus.qza --p-perc-identity 0.99 --o-clustered-table table-cr-99.qza --o-clustered-sequences sequences-cr-99.qza --o-unmatched-sequences umnatched-cr-99.qza.
Now the command is running from almost 32 hours and continuing.
My concern is does it really take that much of times.
Second if the command runs successfully
what I have to do further to get relative abundance table and rep.seq. fileExampleOtuTable.csv (33.0 KB) ExampleOtuTable.csv (33.0 KB) these two types of files and the alpha diversity matrices.

Hi @divyaprince321,

Yes, OTU clustering can take a long time. It all depends on the size of the query and the reference, but in general taking a day or two is not uncommon at all (and it can take longer in some cases).

I have already answered that question here:

though if you are looking for a way to get the CSVs, see the exporting documentation:

See also the tutorials at for more tutorials and information, e.g., how to perform alpha diversity analyses.