# Picrust support?

**URL:** https://forum.qiime2.org/t/picrust-support/1376
**Category:** User Support
**Tags:** closed-reference, otus, vsearch, picrust, export
**Created:** [October 2, 2017, 12:56pm UTC](https://forum.qiime2.org/t/picrust-support/1376 "2017-10-02T12:56:16Z")
**Posts on this page:** 1
**Showing post:** 24

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### Author: ![jjmmii](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/j/f475e1/32.png) [@jjmmii](https://forum.qiime2.org/u/jjmmii)
#### Post date: [November 13, 2017, 2:55am UTC](https://forum.qiime2.org/t/picrust-support/1376/24 "2017-11-13T02:55:23Z")

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Thank you @wasade and @colinbrislawn for your comments. Will definitely try DADA2 -\> ASR but still like to know what happened to my vsearch run.

@wasade, I made a mistake in counting the % recruitment. I reran several parameters and my updated stats are described below:

Firstly, my data is here: (link removed) (730.3 KB) And here are my [clustered\_table.qzv](https://cdck-file-uploads-global.s3.dualstack.us-west-2.amazonaws.com/flex002/uploads/qiime21/original/1X/e07cb2be34602c9018d8eb9568c85fdca1ef8aca.qzv) (343.8 KB) and [unmatched\_sequences.qzv](https://cdck-file-uploads-global.s3.dualstack.us-west-2.amazonaws.com/flex002/uploads/qiime21/original/1X/d9d8b115b1a21188d641aed85e82437e25bb9bb9.qzv) (1.5 MB) from my Greengenes 99otu --p-perc-identity 1 run. My vsearch command is  
`qiime vsearch cluster-features-closed-reference --i-sequences rep-seqss/rep-seqs_subbatch-1.trunc430_ee6.qza --i-table tables/table_subbatch-1.trunc430_ee6.qza --i-reference-sequences 99_otus.qza --p-perc-identity 1 --p-threads 0 --output-dir closedRef_forPICRUSt_subbatch-1`

In clustered\_table.qzv, it says the Number of features is 1383, I count this as the number of recruited features. For the unrecruited features, I don't know how to directly count them. I used a theoretical maximum number of features by running 99\_otus using a very low --p-perc-identity 0.8, so that all reads are clustered (i.e. unmatched\_sequences.qza is empty), and subtracted using this number. Please see this table (and a lazy graph) for the results of my benchmarking:

 ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/1X/175d01514314e886758c1fb66e54d2f3906b2dff.png)

For example, the maximum number of OTUs for 99\_otus is 3825 (trial 4), when running with --p-perc-identity 1, the % recruitment is 1383/(1383+2442) = 36%.

The 16% I previously reported was because I counted the number of unrecruited features by exporting unmatched\_sequences.qzv to get a dna-sequences.fasta file (please get this by viewing unmatched\_sequences.qzv and downloading FASTA from there), then made sure it doesn't contain duplicate sequences, then simply counted the number of sequences, which equals 7319. So the old % recruitment was 1383/(1383+7319) = 16% but that is now obviously wrong (I found out because the sum of number of unrecruited and recruited features is inconsistent across different --p-perc-identity).

You may have noticed in the name of my rep-seqs file that I allowed --p-max-ee 6 in the reads, would this have affected your estimation?  
I am using Greengenes 13\_8.  
In the vsearch command, the --i-reference-sequences is from gg\_13\_8\_otus/rep\_set/99\_otus.fasta .

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