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.
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 https://docs.qiime2.org/2020.11/tutorials/ for more tutorials and information, e.g., how to perform alpha diversity analyses.