qiime2 OTU picking with hundreds of samples

[MichelaRiba (michela)]

Hi,

I am running VSEARCH closed reference OTU picking, it seems again to be very slow with the complete dataset, total of 8,119,151 sequences (after quality filtering and de-replication).
I link this post, where it seems that vsearch classification may be slower than other methodologies

Problem in assigning taxonomy using VSEARCH consensus taxonomy classifier

Thanks @ebolyen. Unfortunately, @Aishiki's results fit with our latest test results. We are currently recommending that users avoid using classify-consensus-vsearch for more than tens of sequences. Fortunately, classify-consensus-blast gives very similar performance to classify-consensus-vsearch in terms of accuracy, but in our tests runs 50 times faster. If run time is still an issue, classify-sklearn was 500 times faster in our tests. There is a tutorial for how to use classify-sklearn here. …

"We are currently recommending that users avoid using classify-consensus-vsearch for more than tens of sequences.

Fortunately, classify-consensus-blast gives very similar performance to classify-consensus-vsearch in terms of accuracy, but in our tests runs 50 times faster. If run time is still an issue, classify-sklearn was 500 times faster in our tests. There is a tutorial for how to use classify-sklearn here ."

May be that my problem in vsearch OTU picking relates to that?

Thanks for your patience

Michela