Hello!
I’ve been attempting the PICRUSt plugin with reference to the various tutorials for exporting files, forum links such as this:
and the main tutorial here
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)
Thanks very much