Qiime2 picrus2 intermediate files

[mashu...@gmail.com]

Hi all,
I have analyzed my dataset with Picrust2 in following way:

Setup_Qiime2Picrust2
qiime2-2019.10 q2-picrust2

Step1

qiime fragment-insertion sepp --i-representative-sequences rep-seqs.qza --p-threads 1 --i-reference-database picrust2_default_sepp_ref.qza --output-dir kangdata_out

Saved Phylogeny[Rooted] to: kangdata_out/tree.qza
Saved Placements to: kangdata_out/placements.qza

Step2
qiime picrust2 custom-tree-pipeline --i-table table.qza --i-tree kangdata_out/tree.qza --p-threads 1 --p-hsp-method pic --p-max-nsti 2 --o-ko-metagenome ko_metagenome_kangdata.qza --o-ec-metagenome ec_metagenome_kangdata.qza --o-pathway-abundance pathway_abundance_kangdata.qza --output-dir q2-picrust2_output_kangdata --verbose

(qiime2-2019.10) msiddiq7@enggpz1p23:~/Kang_dataset_picrust$ qiime picrust2 custom-tree-pipeline --i-table table.qza --i-tree kangdata_out/tree.qza --p-threads 1 --p-hsp-method pic --p-max-nsti 2 --o-ko-metagenome ko_metagenome_kangdata.qza --o-ec-metagenome ec_metagenome_kangdata.qza --o-pathway-abundance pathway_abundance_kangdata.qza --output-dir q2-picrust2_output_kangdata --verbose
Running the below commands:
hsp.py -i 16S -t /tmp/tmpvbdzbv0s/placed_seqs.tre -p 1 -n -o /tmp/tmpvbdzbv0s/picrust2_out/16S_predicted.tsv.gz -m pic

hsp.py -i EC -t /tmp/tmpvbdzbv0s/placed_seqs.tre -p 1 -n -o /tmp/tmpvbdzbv0s/picrust2_out/EC_predicted.tsv.gz -m pic

hsp.py -i KO -t /tmp/tmpvbdzbv0s/placed_seqs.tre -p 1 -n -o /tmp/tmpvbdzbv0s/picrust2_out/KO_predicted.tsv.gz -m pic

metagenome_pipeline.py -i /tmp/tmpvbdzbv0s/intable.biom -f /tmp/tmpvbdzbv0s/picrust2_out/EC_predicted.tsv.gz -o /tmp/tmpvbdzbv0s/picrust2_out/EC_metagenome_out --max_nsti 2.0 -m /tmp/tmpvbdzbv0s/picrust2_out/16S_predicted.tsv.gz
97 of 2393 ASVs were above the max NSTI cut-off of 2.0 and were removed.
97 of 2393 ASVs were above the max NSTI cut-off of 2.0 and were removed.

metagenome_pipeline.py -i /tmp/tmpvbdzbv0s/intable.biom -f /tmp/tmpvbdzbv0s/picrust2_out/KO_predicted.tsv.gz -o /tmp/tmpvbdzbv0s/picrust2_out/KO_metagenome_out --max_nsti 2.0 -m /tmp/tmpvbdzbv0s/picrust2_out/16S_predicted.tsv.gz
97 of 2393 ASVs were above the max NSTI cut-off of 2.0 and were removed.
97 of 2393 ASVs were above the max NSTI cut-off of 2.0 and were removed.

pathway_pipeline.py -i /tmp/tmpvbdzbv0s/picrust2_out/EC_metagenome_out/pred_metagenome_unstrat.tsv.gz -o /tmp/tmpvbdzbv0s/picrust2_out/pathways_out -p 1

Saved FeatureTable[Frequency] to: ko_metagenome_kangdata.qza
Saved FeatureTable[Frequency] to: ec_metagenome_kangdata.qza
Saved FeatureTable[Frequency] to: pathway_abundance_kangdata.qza
(qiime2-2019.10) msiddiq7@enggpz1p23:~/Kang_dataset_picrust$

then Step3> Step4>Step5>
Step6

This command will convert a BIOM file to plain-text, which for the pathway abundance table would look like this:

biom convert -i pathabun_exported_1653kangdata/feature-table_1653.biom -o pathabun_exported_1653kangdata/feature-table.biom_1653kangdata.tsv --to-tsv

My Question:
To analyze further I need to get the files:
placed_seqs.tre, EC_predicted.tsv.gz, KO_predicted.tsv.gz, 16S_predicted.tsv.gz, pred_metagenome_unstrat.tsv.gz

ref: Analysis of qiime2-picrust2 plugin output - #8 by SetaPark 1
but I can’t find those files during analysis.
Maybe, my question is too silly or I am not understanding something!
Your suggestion /instructions will be really appreciated.
Thanks in advance

[Gavin Douglas]

Hey there,

If you want to use those intermediate files you’ll need to run the standalone version of PICRUSt2, see: https://github.com/picrust/picrust2/wiki/PICRUSt2-Tutorial-(v2.3.0-beta)

You can use the tree you already made with SEPP though and skip the place_seqs.py step.

Cheers,

Gavin

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