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Installation
Robyn Wright edited this page May 20, 2025
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PICRUSt2 is available as a standalone version or as a QIIME 2 plugin (which has less functionality than the standalone). Both versions will work on Linux and Mac OS X (although see the note about installing on a Mac below). To use this program on Windows you would first need to install a Linux emulator.
Please note that placing ASVs with the default pipeline and generating stratified output tables with the PICRUSt2 pipeline (predictions broken down by contributing sequences) requires more computing resources than the PICRUSt1 metagenome prediction steps. You will need at least 16 GB of RAM and the running time may be several hours depending on how many CPUs you can dedicate (and how many samples and sequences are input).
Note that there are fewer options currently available for the QIIME2 plugin, but there are lower memory requirements if a non-default method is used for placing ASVs into a reference tree (which is described in the tutorial). A tutorial on this QIIME2 plugin is available here and the alternative installation instructions for installation and use of PICRUSt2 with this plugin are here.
You can install PICRUSt2 either with conda or from source, which are both shown below. Note that both approaches require that you first install conda. We also recommend that users use the mamba package, which is a reimplementation of conda in C++, which typically increases the installation time substantially (the default conda can sometimes get stuck solving environments for hours at a time, which is a problem facing conda environments in general). You do not need to use mamba though, you can just replace mamba in the below commands with conda to use the standard conda approach.
Create a new environment with PICRUSt2 installed and activate the environment.
mamba create -n picrust2 -c bioconda -c conda-forge picrust2=2.6.2
After installation you need to activate the conda environment:
mamba activate picrust2
Note: If you had installed PICRUSt2 using mamba/conda prior to 14th May 2025, you may be missing some of the default reference files. This is now fixed in v2.6.2 that is available from bioconda. This did not affect installations from source.
Download the source tarball, untar, and move into directory. You can check that you are downloading the latest release here: https://github.com/picrust/picrust2/releases
wget https://github.com/picrust/picrust2/archive/v2.6.2.tar.gz
tar xvzf v2.6.2.tar.gz
cd picrust2-2.6.2/
Create and activate the environment (with requirements) and then install PICRUSt2 with pip.
mamba env create -f picrust2-env.yaml
mamba activate picrust2
pip install --editable .
Run the tests to verify the installation (note that this wont work if you followed the bioconda install instructions, unless you also downloaded the source code and navigated to the main directory):
pytest
We have heard of several users having issues installing PICRUSt2 on Macs with M1/M2/M3 processors. These seem to be due to several different compatibility/version issues, but what is currently working for us is installation from source as follows:
wget https://github.com/picrust/picrust2/archive/v2.6.2.tar.gz
tar xvzf v2.6.2.tar.gz
cd picrust2-2.6.2/
mamba env create -f picrust2-env.yaml --platform osx-64 python=3.10
mamba activate picrust2
pip install --editable .
The pytest command currently tests that the installation as a whole is working, but we have had some issues with reference data missing. We have a very small dataset (37 sequences) that you can download and test PICRUSt2 on if you like.
Download and unzip the files:
wget http://kronos.pharmacology.dal.ca/public_files/picrust/picrust2_tutorial_files/chemerin_16S_arc.tar.gz
tar -xvf chemerin_16S_arc.tar.gz
Run PICRUSt2:
picrust2_pipeline.py -s chemerin_16S_arc/seqs_arc.fna -i chemerin_16S_arc/table.biom -o picrust2_out_pipeline -p 1 --verbose
On my M1 16GB RAM MacBook Air, this took about 25 mins to run with 6 threads.
37 of 37 sequence ids overlap between input table and FASTA.
37 ASVs in the input FASTA. None of the sequence ids are duplicated.
Placing sequences onto reference tree
place_seqs.py --study_fasta chemerin_16S_arc/seqs_arc.fna --ref_dir /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/bacteria/bac_ref --out_tree picrust2_out_pipeline/bac.tre --processes 6 --intermediate picrust2_out_pipeline/intermediate/place_seqs_bac --min_align 0.8 --chunk_size 5000 --placement_tool epa-ng --verbose
INFO Selected: Output dir: picrust2_out_pipeline/intermediate/place_seqs_bac/epa_out/
INFO Selected: Query file: picrust2_out_pipeline/intermediate/place_seqs_bac/study_seqs_hmmalign.fasta
INFO Selected: Tree file: /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/bacteria/bac_ref/bac_ref.tre
INFO Selected: Reference MSA: picrust2_out_pipeline/intermediate/place_seqs_bac/ref_seqs_hmmalign.fasta
INFO Selected: Filtering by accumulated threshold: 0.99
INFO Selected: Maximum number of placements per query: 100
INFO Selected: Automatic switching of use of per rate scalers
INFO Selected: Preserving the root of the input tree
INFO Selected: Specified model file: /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/bacteria/bac_ref/bac_ref.model
INFO Selected: Reading queries in chunks of: 5000
INFO Selected: Using threads: 6
INFO ______ ____ ___ _ __ ______
/ ____// __ \ / | / | / // ____/
/ __/ / /_/ // /| | ______ / |/ // / __
/ /___ / ____// ___ |/_____// /| // /_/ /
/_____//_/ /_/ |_| /_/ |_/ \____/ (v0.3.8)
INFO Using model parameters:
INFO Rate heterogeneity: GAMMA (4 cats, mean), alpha: 0.408013 (user), weights&rates: (0.25,0.0178872) (0.25,0.187716) (0.25,0.739808) (0.25,3.05459)
Base frequencies (user): 0.209289 0.232667 0.311531 0.246513
Substitution rates (user): 1.04872 2.92815 1.63887 0.831209 3.68952 1
INFO Output file: picrust2_out_pipeline/intermediate/place_seqs_bac/epa_out/epa_result.jplace
INFO 37 Sequences done!
INFO Time spent placing: 58s
INFO Elapsed Time: 73s
.... ....
'' '||. .||'
|| ||
'|.|'
...' .... ... ... ... ... .... .|'|.
| || '' .|| ||' || ||' || '' .|| .|' ||
|'' .|' || || | || | .|' || .|'|. ||
'.... '|..'|'. ||...' ||...' '|..'|. '||' ||:.
'....' || ||
'''' '''' v0.9.0 (c) 2017-2025
by Lucas Czech and Pierre Barbera
Invocation: gappa examine graft --jplace-path picrust2_out_pipeline/intermediate/place_seqs_bac/epa_out/epa_result_parsed.jplace --fully-resolve --out-dir picrust2_out_pipeline/intermediate/place_seqs_bac/epa_out
Command: gappa examine graft
Input:
--jplace-path picrust2_out_pipeline/intermediate/place_seqs_bac/epa_out/epa_result_parsed.jplace
Settings:
--fully-resolve true
--name-prefix
Output:
--out-dir picrust2_out_pipeline/intermediate/place_seqs_bac/epa_out
--file-prefix
--file-suffix
Newick Tree Output:
--newick-tree-quote-invalid-chars
false
Global Options:
--allow-file-overwriting false
--verbose false
--threads 8
--log-file
Run the following command to get the references that need to be cited:
`gappa tools citation Czech2020-genesis-and-gappa`
Started 2025-05-20 11:56:05
Found 1 jplace file
Finished 2025-05-20 11:56:05
hmmalign --trim --dna --mapali /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/bacteria/bac_ref/bac_ref.fna --informat FASTA -o picrust2_out_pipeline/intermediate/place_seqs_bac/query_align.stockholm /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/bacteria/bac_ref/bac_ref.hmm chemerin_16S_arc/seqs_arc.fna
Raw input sequences ranged in length from 359 to 400
epa-ng --tree /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/bacteria/bac_ref/bac_ref.tre --ref-msa picrust2_out_pipeline/intermediate/place_seqs_bac/ref_seqs_hmmalign.fasta --query picrust2_out_pipeline/intermediate/place_seqs_bac/study_seqs_hmmalign.fasta --chunk-size 5000 -T 6 -m /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/bacteria/bac_ref/bac_ref.model -w picrust2_out_pipeline/intermediate/place_seqs_bac/epa_out --filter-acc-lwr 0.99 --filter-max 100
gappa examine graft --jplace-path picrust2_out_pipeline/intermediate/place_seqs_bac/epa_out/epa_result_parsed.jplace --fully-resolve --out-dir picrust2_out_pipeline/intermediate/place_seqs_bac/epa_out
mv picrust2_out_pipeline/intermediate/place_seqs_bac/epa_out/epa_result_parsed.newick picrust2_out_pipeline/bac.tre
Finished placing sequences on output tree for reference 1: picrust2_out_pipeline/bac.tre
place_seqs.py --study_fasta chemerin_16S_arc/seqs_arc.fna --ref_dir /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/archaea/arc_ref --out_tree picrust2_out_pipeline/arc.tre --processes 6 --intermediate picrust2_out_pipeline/intermediate/place_seqs_arc --min_align 0.8 --chunk_size 5000 --placement_tool epa-ng --verbose
INFO Selected: Output dir: picrust2_out_pipeline/intermediate/place_seqs_arc/epa_out/
INFO Selected: Query file: picrust2_out_pipeline/intermediate/place_seqs_arc/study_seqs_hmmalign.fasta
INFO Selected: Tree file: /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/archaea/arc_ref/arc_ref.tre
INFO Selected: Reference MSA: picrust2_out_pipeline/intermediate/place_seqs_arc/ref_seqs_hmmalign.fasta
INFO Selected: Filtering by accumulated threshold: 0.99
INFO Selected: Maximum number of placements per query: 100
INFO Selected: Automatic switching of use of per rate scalers
INFO Selected: Preserving the root of the input tree
INFO Selected: Specified model file: /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/archaea/arc_ref/arc_ref.model
INFO Selected: Reading queries in chunks of: 5000
INFO Selected: Using threads: 6
INFO ______ ____ ___ _ __ ______
/ ____// __ \ / | / | / // ____/
/ __/ / /_/ // /| | ______ / |/ // / __
/ /___ / ____// ___ |/_____// /| // /_/ /
/_____//_/ /_/ |_| /_/ |_/ \____/ (v0.3.8)
INFO Using model parameters:
INFO Rate heterogeneity: GAMMA (4 cats, mean), alpha: 0.509646 (user), weights&rates: (0.25,0.0351892) (0.25,0.258166) (0.25,0.827162) (0.25,2.87948)
Base frequencies (user): 0.224411 0.252166 0.284495 0.238928
Substitution rates (user): 1.16611 4.36836 1.83214 1.0193 5.96274 1
INFO Output file: picrust2_out_pipeline/intermediate/place_seqs_arc/epa_out/epa_result.jplace
INFO 37 Sequences done!
INFO Time spent placing: 0s
INFO Elapsed Time: 1s
.... ....
'' '||. .||'
|| ||
'|.|'
...' .... ... ... ... ... .... .|'|.
| || '' .|| ||' || ||' || '' .|| .|' ||
|'' .|' || || | || | .|' || .|'|. ||
'.... '|..'|'. ||...' ||...' '|..'|. '||' ||:.
'....' || ||
'''' '''' v0.9.0 (c) 2017-2025
by Lucas Czech and Pierre Barbera
Invocation: gappa examine graft --jplace-path picrust2_out_pipeline/intermediate/place_seqs_arc/epa_out/epa_result_parsed.jplace --fully-resolve --out-dir picrust2_out_pipeline/intermediate/place_seqs_arc/epa_out
Command: gappa examine graft
Input:
--jplace-path picrust2_out_pipeline/intermediate/place_seqs_arc/epa_out/epa_result_parsed.jplace
Settings:
--fully-resolve true
--name-prefix
Output:
--out-dir picrust2_out_pipeline/intermediate/place_seqs_arc/epa_out
--file-prefix
--file-suffix
Newick Tree Output:
--newick-tree-quote-invalid-chars
false
Global Options:
--allow-file-overwriting false
--verbose false
--threads 8
--log-file
Run the following command to get the references that need to be cited:
`gappa tools citation Czech2020-genesis-and-gappa`
Started 2025-05-20 11:56:12
Found 1 jplace file
Finished 2025-05-20 11:56:12
hmmalign --trim --dna --mapali /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/archaea/arc_ref/arc_ref.fna --informat FASTA -o picrust2_out_pipeline/intermediate/place_seqs_arc/query_align.stockholm /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/archaea/arc_ref/arc_ref.hmm chemerin_16S_arc/seqs_arc.fna
Raw input sequences ranged in length from 359 to 400
epa-ng --tree /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/archaea/arc_ref/arc_ref.tre --ref-msa picrust2_out_pipeline/intermediate/place_seqs_arc/ref_seqs_hmmalign.fasta --query picrust2_out_pipeline/intermediate/place_seqs_arc/study_seqs_hmmalign.fasta --chunk-size 5000 -T 6 -m /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/archaea/arc_ref/arc_ref.model -w picrust2_out_pipeline/intermediate/place_seqs_arc/epa_out --filter-acc-lwr 0.99 --filter-max 100
gappa examine graft --jplace-path picrust2_out_pipeline/intermediate/place_seqs_arc/epa_out/epa_result_parsed.jplace --fully-resolve --out-dir picrust2_out_pipeline/intermediate/place_seqs_arc/epa_out
mv picrust2_out_pipeline/intermediate/place_seqs_arc/epa_out/epa_result_parsed.newick picrust2_out_pipeline/arc.tre
Finished placing sequences on output tree for reference 2: picrust2_out_pipeline/arc.tre
hsp.py --tree picrust2_out_pipeline/bac.tre --output picrust2_out_pipeline/bac_marker_predicted_and_nsti.tsv.gz --observed_trait_table /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/bacteria/16S.txt.gz --hsp_method mp --edge_exponent 0.5 --seed 100 --calculate_NSTI --processes 1 --verbose
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_nsti.R picrust2_out_pipeline/bac.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkq0l2vyx/known_tips.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkq0l2vyx/nsti_out.txt
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp3ceezlw1/subset_tab_0 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp_dx9s92g/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp_dx9s92g/predicted_ci.txt 100
hsp.py --tree picrust2_out_pipeline/arc.tre --output picrust2_out_pipeline/arc_marker_predicted_and_nsti.tsv.gz --observed_trait_table /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/archaea/16S.txt.gz --hsp_method mp --edge_exponent 0.5 --seed 100 --calculate_NSTI --processes 1 --verbose
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_nsti.R picrust2_out_pipeline/arc.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp7dd5bu38/known_tips.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp7dd5bu38/nsti_out.txt
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmplklakx48/subset_tab_0 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpzofc4adj/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpzofc4adj/predicted_ci.txt 100
Finished getting marker and NSTI predictions for both domains: picrust2_out_pipeline/bac_marker_predicted_and_nsti.tsv.gz, picrust2_out_pipeline/arc_marker_predicted_and_nsti.tsv.gz
Now finding the best one for each sequence.
Picking the best domains for all sequences.
35 sequences were kept for bac
2 sequences were kept for arc
Finished getting the best domain match for each sequence: picrust2_out_pipeline/combined_marker_predicted_and_nsti.tsv.gz Now running hsp.py for the reduced reference sets.
hsp.py --tree picrust2_out_pipeline/bac_reduced.tre --output picrust2_out_pipeline/bac_EC_predicted.tsv.gz --observed_trait_table /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/bacteria/ec.txt.gz --hsp_method mp --edge_exponent 0.5 --seed 100 --processes 6 --verbose
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpthp0qvwo/subset_tab_0 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpun2pptb7/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpun2pptb7/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpthp0qvwo/subset_tab_1 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpdxk4e2vk/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpdxk4e2vk/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpthp0qvwo/subset_tab_2 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpviniacic/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpviniacic/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpthp0qvwo/subset_tab_3 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp1aq133os/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp1aq133os/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpthp0qvwo/subset_tab_4 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpubsu7r62/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpubsu7r62/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpthp0qvwo/subset_tab_5 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpuklg8pi0/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpuklg8pi0/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpthp0qvwo/subset_tab_6 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxsw2k6w5/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxsw2k6w5/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpthp0qvwo/subset_tab_7 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpv6314tg_/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpv6314tg_/predicted_ci.txt 100
hsp.py --tree picrust2_out_pipeline/bac_reduced.tre --output picrust2_out_pipeline/bac_KO_predicted.tsv.gz --observed_trait_table /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/bacteria/ko.txt.gz --hsp_method mp --edge_exponent 0.5 --seed 100 --processes 6 --verbose
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_2 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmppr83fod3/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmppr83fod3/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_0 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmppud4vagt/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmppud4vagt/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_1 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpg5f040tx/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpg5f040tx/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_3 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmphrx_fz3j/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmphrx_fz3j/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_4 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp0jnawcrs/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp0jnawcrs/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_5 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpm7bqjejp/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpm7bqjejp/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_6 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpawis9zpq/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpawis9zpq/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_7 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxjawecwn/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxjawecwn/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_8 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp31o630v5/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp31o630v5/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_9 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp9gnkr_2n/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp9gnkr_2n/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_10 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpu8sp8ydn/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpu8sp8ydn/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_11 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpwyraw_3l/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpwyraw_3l/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_12 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpa0mms8nv/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpa0mms8nv/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_13 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpnlbg17ll/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpnlbg17ll/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_14 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp8pouhutv/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp8pouhutv/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_15 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpoinu748i/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpoinu748i/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_16 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp4sjk9pve/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp4sjk9pve/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_17 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmperquvgw0/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmperquvgw0/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_18 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkk7qa5_7/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkk7qa5_7/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_19 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp6ju435yx/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp6ju435yx/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_20 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpb7m3r6ci/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpb7m3r6ci/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_21 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmprxz5svlr/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmprxz5svlr/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_22 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpt7klifws/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpt7klifws/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_23 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp36pqoxdk/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp36pqoxdk/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_24 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpupme4fay/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpupme4fay/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_25 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxu635y4l/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxu635y4l/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_26 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmphrlbqhg4/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmphrlbqhg4/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/bac_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpxdaz4hnn/subset_tab_27 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpethjsc4i/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpethjsc4i/predicted_ci.txt 100
hsp.py --tree picrust2_out_pipeline/arc_reduced.tre --output picrust2_out_pipeline/arc_EC_predicted.tsv.gz --observed_trait_table /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/archaea/ec.txt.gz --hsp_method mp --edge_exponent 0.5 --seed 100 --processes 6 --verbose
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmphzko6l3n/subset_tab_0 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp1hl08s5r/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp1hl08s5r/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmphzko6l3n/subset_tab_1 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp507sixjm/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp507sixjm/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmphzko6l3n/subset_tab_3 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpn8blwtq9/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpn8blwtq9/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmphzko6l3n/subset_tab_4 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkwt17xu0/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkwt17xu0/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmphzko6l3n/subset_tab_2 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp02o77rnj/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp02o77rnj/predicted_ci.txt 100
hsp.py --tree picrust2_out_pipeline/arc_reduced.tre --output picrust2_out_pipeline/arc_KO_predicted.tsv.gz --observed_trait_table /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/archaea/ko.txt.gz --hsp_method mp --edge_exponent 0.5 --seed 100 --processes 6 --verbose
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_0 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpebfj6omh/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpebfj6omh/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_2 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpwnnerby_/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpwnnerby_/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_1 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpgk0dk4ac/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpgk0dk4ac/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_3 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpre_zs3ee/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpre_zs3ee/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_4 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpyvhiimh3/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpyvhiimh3/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_5 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpw21970hv/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpw21970hv/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_6 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpdz0kmuoj/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpdz0kmuoj/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_7 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpaq4ltvwe/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpaq4ltvwe/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_8 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpia4ft5ll/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpia4ft5ll/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_9 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpgcsor8ql/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpgcsor8ql/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_10 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp6f2_ximg/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp6f2_ximg/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_11 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpd8aaeks5/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpd8aaeks5/predicted_ci.txt 100
Rscript /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/Rscripts/castor_hsp.R picrust2_out_pipeline/arc_reduced.tre /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmpkd2wdr2i/subset_tab_12 mp 0.5 FALSE FALSE /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp9heq2g1q/predicted_counts.txt /var/folders/fw/w98nh67x43l6tcs4c_pxwgmh0000gn/T/tmp9heq2g1q/predicted_ci.txt 100
Finished getting functional predictions for all traits.
['bac_KO', 'arc_KO'] {'bac_marker': 'picrust2_out_pipeline/bac_reduced_marker_predicted_and_nsti.tsv.gz', 'arc_marker': 'picrust2_out_pipeline/arc_reduced_marker_predicted_and_nsti.tsv.gz', 'bac_EC': 'picrust2_out_pipeline/bac_EC_predicted.tsv.gz', 'bac_KO': 'picrust2_out_pipeline/bac_KO_predicted.tsv.gz', 'arc_EC': 'picrust2_out_pipeline/arc_EC_predicted.tsv.gz', 'arc_KO': 'picrust2_out_pipeline/arc_KO_predicted.tsv.gz'}
['bac_EC', 'arc_EC'] {'bac_marker': 'picrust2_out_pipeline/bac_reduced_marker_predicted_and_nsti.tsv.gz', 'arc_marker': 'picrust2_out_pipeline/arc_reduced_marker_predicted_and_nsti.tsv.gz', 'bac_EC': 'picrust2_out_pipeline/bac_EC_predicted.tsv.gz', 'bac_KO': 'picrust2_out_pipeline/bac_KO_predicted.tsv.gz', 'arc_EC': 'picrust2_out_pipeline/arc_EC_predicted.tsv.gz', 'arc_KO': 'picrust2_out_pipeline/arc_KO_predicted.tsv.gz'}
Finished joining together all trait tables with the same trait name for both domains.
Running metagenome pipeline for KO
metagenome_pipeline.py --input chemerin_16S_arc/table.biom --function picrust2_out_pipeline/combined_KO_predicted.tsv.gz --min_reads 1 --min_samples 1 --out_dir picrust2_out_pipeline/KO_metagenome_out --max_nsti 2.0 --marker picrust2_out_pipeline/combined_marker_predicted_and_nsti.tsv.gz
All ASVs were below the max NSTI cut-off of 2.0 and so all were retained for downstream analyses.
Running metagenome pipeline for EC
metagenome_pipeline.py --input chemerin_16S_arc/table.biom --function picrust2_out_pipeline/combined_EC_predicted.tsv.gz --min_reads 1 --min_samples 1 --out_dir picrust2_out_pipeline/EC_metagenome_out --max_nsti 2.0 --marker picrust2_out_pipeline/combined_marker_predicted_and_nsti.tsv.gz
All ASVs were below the max NSTI cut-off of 2.0 and so all were retained for downstream analyses.
Inferring pathways from predicted EC
pathway_pipeline.py --input picrust2_out_pipeline/EC_metagenome_out/pred_metagenome_unstrat.tsv.gz --out_dir picrust2_out_pipeline/pathways_out --map /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/pathway_mapfiles/metacyc_pathways_structured_filtered_v24.txt --intermediate picrust2_out_pipeline/intermediate/pathways --proc 6 --regroup_map /Users/robynwright/Dropbox/Langille_Lab_postdoc/Github/picrust2-2.6.2/picrust2/default_files/pathway_mapfiles/ec_level4_to_metacyc_rxn_new.tsv --verbose
Wrote predicted pathway abundances and coverages to picrust2_out_pipeline/pathways_out
Completed PICRUSt2 pipeline in 1559.08 seconds.
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