PICRUSt artifacts

[Cybele_C]

Hello!

I’ve been attempting the PICRUSt plugin with reference to the various tutorials for exporting files, forum links such as this:

Picrust support?

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 (343.8 KB) and unmatched_sequences.qzv (1.5 MB) from my Greengenes 99otu --p-perc-identity 1 run. My vsearch command is qiime vsearch clu…

and the main tutorial here

picrust/picrust2

I have this, so far: qiime vsearch cluster-features-closed-reference \

–i-table table3.qza
–i-sequences rep-seqs3.qza
–i-reference-sequences gg_13_5_otu_97.qza
–p-perc-identity 0.97
–o-clustered-table table-cr-97.qza
–o-clustered-sequences rep-seqs-cr-97.qza
–o-unmatched-sequences unmatched-cr-97.qza

Saved FeatureTable[Frequency] to: table-cr-97.qza
Saved FeatureData[Sequence] to: rep-seqs-cr-97.qza
Saved FeatureData[Sequence] to: unmatched-cr-97.qza

But I’ve tried this code without results:
qiime fragment-insertion sepp --i-representative-sequences rep-seqs-cr-97.qza
–p-threads 1 --i-reference-alignment reference.fna.qza
–i-reference-phylogeny reference.tre.qza
–output-dir tutorial_placed_out

• I understood from the tutorial that the .fna file and .tre artifacts were provided, presumably in the plugin? I have the rep-sees file in the same directory as the plugin, but not the same folders.

Also, this page seems to reference the first QIIME, so I used instructions from the support forum thread for the files above (from Gil Sharon)

@gmdouglas

Thanks very much

[gmdouglas]

Hi @Cybele_C,

I think there are a few things going on here. Firstly, that first thread you referred to discusses how to run PICRUSt1 with QIIME2-outputted files. This is no longer required since you can use the PICRUSt2 plugin with QIIME2 (i.e. there’s no need to do closed reference OTU picking).

If the error you got was related to reference.fna.qza and reference.tre.qza missing then indeed you will need to acquire these files. You’ll need to download these files, which is done during the q2-picrust2 tutorial.

Also, this page seems to reference the first QIIME, so I used instructions from the support forum thread for the files above (from Gil Sharon)

I’m not sure what page you’re referring to here - would you mind clarifying?

Thanks,

Gavin

[Cybele_C]

Hi Gavin - I had assumed that the tutorial files were all relevant just for the tutorial, so I moved the files from the test folder to my working folder and all has been smooth from there. Thank you so much for your help and work!

[system]

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