# Qiime2 picrus2 intermediate files
**URL:** https://forum.qiime2.org/t/qiime2-picrus2-intermediate-files/18896
**Category:** Library Support
**Created:** [March 17, 2021, 6:31pm UTC](https://forum.qiime2.org/t/qiime2-picrus2-intermediate-files/18896 "2021-03-17T18:31:48Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@Mashuk](https://forum.qiime2.org/u/Mashuk)
#### Post date: [March 17, 2021, 6:31pm UTC](https://forum.qiime2.org/t/qiime2-picrus2-intermediate-files/18896/1 "2021-03-17T18:31:48Z")
Hi all,
I have analyzed my dataset with Picrust2 in following way:
Setup\_Qiime2Picrust
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](https://forum.qiime2.org/t/analysis-of-qiime2-picrust2-plugin-output/13392/8)
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 helpful.
Thanks in advance
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [April 18, 2021, 12:32am UTC](https://forum.qiime2.org/t/qiime2-picrus2-intermediate-files/18896/2 "2021-04-18T00:32:41Z")
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