Regarding running cluster-feature-closed-reference

[divyaprince321 (divya)]

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.

[Nicholas_Bokulich]

Hi @divyaprince321,

@divyaprince321

Now the command is running from almost 32 hours and continuing.
My concern is does it really take that much of times.

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).

@divyaprince321

what I have to do further to get relative abundance table and rep.seq. fileExampleOtuTable.csv (33.0 KB) ExampleOtuTable.csv (33.0 KB)

I have already answered that question here:

Importing sequence files (.fna) files

That is correct. You can search the forum archive to see how others have addressed this same error. Unfortunately, allocating more memory to the virtual box and using a more powerful computer may be your only options. The help documentation for all QIIME 2 actions details the outputs and their content. E.g., for this action type this into the terminal and hit enter: qiime vsearch cluster-features-closed-reference --help Among other details, you will see this: Outputs: --o-clustered-table…

though if you are looking for a way to get the CSVs, see the exporting documentation:
https://docs.qiime2.org/2020.11/tutorials/exporting/

See also the tutorials at Tutorials — QIIME 2 2020.11.1 documentation for more tutorials and information, e.g., how to perform alpha diversity analyses.