.fna file in picrust2 in qiime2

import

(Nilam) #1

I want to use picrust2 in qiime2. But it requires .fna file. So i cant understand how to generate .fna file.
And i have one doubt that .fna file generated in qiime1 can i use this file in qiime2? Please help me in this doubt.

Thanks in advance


(Matthew Ryan Dillon) #2

Have you checked out the q2-picrust2 plugin? This will allow you to directly interface with picrust2 using QIIME 2 Artifacts. Thanks! :qiime2: :t_rex:


#3

I think that I have the same question - the code for an .fna file is from the main tutorial on the q2-picrust2 plugin. My codes were:
$ 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

  • then the issue:
    $ 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

Usage: qiime fragment-insertion sepp [OPTIONS]
Try “qiime fragment-insertion sepp --help” for help.

Error: Invalid value for “–i-reference-alignment”: File “reference.fna.qza” does not exist.

Thanks very much in advance -


(Matthew Ryan Dillon) #4

Hey there @Cybele_C!

This error means you don’t have a file by that name in your current working directory. Do you have a reference alignment in your current working directory?