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Welcome! This group is for discussing and asking questions about PICRUSt and PICRUSt2.

If your question is about PICRUSt2 please first check the Frequently Asked Questions page.

In addition, please search the previous messages (in the search bar above) before asking your question.

If you are reporting an error please report the exact tool version, command run, and error message.

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Alejandro Rosas Lopez

Apr 22

Error of visualization of picrust functional prediction results on RStudio

Hi everyone. I'm new in this magical worl. I've peformed a pipeline of Picrust for functional

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Error of visualization of picrust functional prediction results on RStudio

Hi everyone. I'm new in this magical worl. I've peformed a pipeline of Picrust for functional

Apr 22

Yannan Huang

Apr 19

I have a question about pathway-level results.

Hi PICRUSt2 group, I am Yannan from Dalhousie University. I am using PICRUSt2 to analyze wastewater

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I have a question about pathway-level results.

Hi PICRUSt2 group, I am Yannan from Dalhousie University. I am using PICRUSt2 to analyze wastewater

Apr 19

Rishikesh Dash, … Allan Amorim Santos5

Apr 3

Facing issue for importing representative sequence file into picrust2

Hi Robyn. I got it. However, I found some new doubts. I run v4 samples following the pipeline

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Facing issue for importing representative sequence file into picrust2

Hi Robyn. I got it. However, I found some new doubts. I run v4 samples following the pipeline

Apr 3

Gonzalo Ferreira, … Robyn Wright3

Apr 1

Error with installation

Hi there, Could you see if the fix mentioned here works? Thanks, Robyn On Monday 1 April 2024 at 16:

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Error with installation

Hi there, Could you see if the fix mentioned here works? Thanks, Robyn On Monday 1 April 2024 at 16:

Apr 1

Allan Amorim Santos

Mar 28

Help with picrust2 using Mothur

Hi everyone, hope you are doing well. I'm a beginner user and I'm working on Mothur for

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Help with picrust2 using Mothur

Hi everyone, hope you are doing well. I'm a beginner user and I'm working on Mothur for

Mar 28

Vincent Darbot

Feb 14

Problem with custom database (place_seqs step)

Hello, To enhance functional predictions for fungal ITS sequences, I am currently constructing a

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Problem with custom database (place_seqs step)

Hello, To enhance functional predictions for fungal ITS sequences, I am currently constructing a

Feb 14

Erica Dasi

Feb 8

Units of functional gene abundance from Picrust2 analysis

Good evening, Hope you are doing well. I have completed my Picrust2 analysis and have a question

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Units of functional gene abundance from Picrust2 analysis

Good evening, Hope you are doing well. I have completed my Picrust2 analysis and have a question

Feb 8

Felipe Melis, Robyn Wright5

Jan 26

Picrust 2 reference alignment

Ok, I understand! Wow, about the new reference, can I offer help with that? I'm very interested

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Picrust 2 reference alignment

Ok, I understand! Wow, about the new reference, can I offer help with that? I'm very interested

Jan 26

Anastasia A. Zabolotneva, Robyn Wright2

Jan 22

Interpretation of gene abundance data

Hi, I'm not quite sure which abundances you're referring to - the abundance of a specific

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Interpretation of gene abundance data

Hi, I'm not quite sure which abundances you're referring to - the abundance of a specific

Jan 22

Rashmi Ira, Robyn Wright2

Jan 22

Import .fq file: Picrust analysis

Hi Rashmi, I take it from your second question that I just answered that you managed to get this

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Import .fq file: Picrust analysis

Hi Rashmi, I take it from your second question that I just answered that you managed to get this

Jan 22

Rashmi Ira, Robyn Wright2

Jan 22

Problem in interprating warnings and results after using qiime picrust2 full-pipeline

Hi there, That means that two of your ASVs (those listed as being excluded) were very different to

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Problem in interprating warnings and results after using qiime picrust2 full-pipeline

Hi there, That means that two of your ASVs (those listed as being excluded) were very different to

Jan 22

Siti Nurmilah, Robyn Wright2

Jan 17

Error Message-Default File

Hi there, That error message is suggesting that the files needed for PICRUSt2 to run aren't

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Error Message-Default File

Hi there, That error message is suggesting that the files needed for PICRUSt2 to run aren't

Jan 17

Samuel David Gamboa-Tuz

Jan 4

Why CIs are no longer supported with the hsp.py script in picrust2?

Hello, I was wondering why CIs are no longer supported with the hsp.py script in picrust2? https://

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Why CIs are no longer supported with the hsp.py script in picrust2?

Hello, I was wondering why CIs are no longer supported with the hsp.py script in picrust2? https://

Jan 4

Samuel David Gamboa-Tuz

Jan 4

Confidence intervals in picrust2

Hello. I was wondeing why Confidence intervals are no longer supported in the hsp.py of picrust2?

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Confidence intervals in picrust2

Hello. I was wondeing why Confidence intervals are no longer supported in the hsp.py of picrust2?

Jan 4

Adams Mabruk, Robyn Wright2

12/11/23

Installation using Conda

Hi there, You should be able to install epa-ng with conda also (see here). You should do this and

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Installation using Conda

Hi there, You should be able to install epa-ng with conda also (see here). You should do this and

12/11/23

Abbi Hernandez, Robyn Wright2

12/6/23

Galaxy no longer has picrust2?

Hi there, I have not personally used the Galaxy server, however, it seems to be available here? I

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Galaxy no longer has picrust2?

Hi there, I have not personally used the Galaxy server, however, it seems to be available here? I

12/6/23

Ana Benavides, Robyn Wright6

12/6/23

Does anyone know how to use PICRUST with the data obtained from Kraken?

Hi Ana, The command you've shown doesn't tell me which files you use for running kraken2, or

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Does anyone know how to use PICRUST with the data obtained from Kraken?

Hi Ana, The command you've shown doesn't tell me which files you use for running kraken2, or

12/6/23

Franek by, Robyn Wright2

12/6/23

Random NAs inserted in the norm_taxon_function_contrib column

Hi Franek, Could you maybe try running the full picrust2_pipeline.py with the --per_sequence_contrib

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Random NAs inserted in the norm_taxon_function_contrib column

Hi Franek, Could you maybe try running the full picrust2_pipeline.py with the --per_sequence_contrib

12/6/23

Rasmita Mishra, … Ana Benavides3

11/28/23

How can I generate ASV file format from nanopore sequencing data for Picrust2 input file?

Hi :), I would like to know if you found a solution? I'm trying to analyze a lot of metabarcoding

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How can I generate ASV file format from nanopore sequencing data for Picrust2 input file?

Hi :), I would like to know if you found a solution? I'm trying to analyze a lot of metabarcoding

11/28/23

Rebecca Brittain, Eduardo Castro3

11/8/23

picrust2 installation error on mac m2

Hi Eduardo, I was not able to resolve this on my mac but I was able to resolve it on our university

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picrust2 installation error on mac m2

Hi Eduardo, I was not able to resolve this on my mac but I was able to resolve it on our university

11/8/23

BHAGYASHRI PODDAR, … Rashmi Ira9

10/18/23

Picrust 2 metagenomic prediction

Hi @Robyn Thank you for your kind response. I will look into it. Thanks a lot. Best Regards, Rashmi

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Picrust 2 metagenomic prediction

Hi @Robyn Thank you for your kind response. I will look into it. Thanks a lot. Best Regards, Rashmi

10/18/23

ROHIT PATEL, Robyn Wright2

10/17/23

ASV with 0 hits filtering

Hi, No, this won't have any negative impact on your analysis, and you should indeed remove any

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ASV with 0 hits filtering

Hi, No, this won't have any negative impact on your analysis, and you should indeed remove any

10/17/23

Khalid IBRAHIM, Robyn Wright2

10/16/23

Hi all and thank you in advance.

Hi Khalid, PICRUSt2 doesn't have any functions for classifying the taxa within your samples, but

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Hi all and thank you in advance.

Hi Khalid, PICRUSt2 doesn't have any functions for classifying the taxa within your samples, but

10/16/23

Maria Bernard

10/10/23

MetaCyc update

Hello there, I saw that Picrust2 relies on MetaCyc files formated for humanN2 (maybe with

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MetaCyc update

Hello there, I saw that Picrust2 relies on MetaCyc files formated for humanN2 (maybe with

10/10/23

Sanya Puri

9/27/23

C-sibelia - 3.0.7

Finding synteny blocks and generating the output... Calling variants... An error occured: Using

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C-sibelia - 3.0.7

Finding synteny blocks and generating the output... Calling variants... An error occured: Using

9/27/23

Felipe Melis

9/6/23

Fungi ko database

Hello, I want to build a custom ko counts database for fungi. So I have the following question. The

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Fungi ko database

Hello, I want to build a custom ko counts database for fungi. So I have the following question. The

9/6/23

BioHazard Dragon, Gavin Douglas3

8/30/23

Need some advice as to why Archaea PICRUSt functions present in QIIME2 data with no Archaea identified

Hi there, The MetaCyc pathways are based on what gene families are predicted to be present. These

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Need some advice as to why Archaea PICRUSt functions present in QIIME2 data with no Archaea identified

Hi there, The MetaCyc pathways are based on what gene families are predicted to be present. These

8/30/23

Malib, Gavin Douglas3

7/14/23

Nanopore sequencing data

Thank you for the response Gavin, I will have a look at the tutorial. On Thursday, July 13, 2023 at 2

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Nanopore sequencing data

Thank you for the response Gavin, I will have a look at the tutorial. On Thursday, July 13, 2023 at 2

7/14/23

ROHIT PATEL

6/26/23

ASV with 0 hits filtering

I have two files as input here in picrust2 analysis: 1. seqs.fna 2. table.biom table.biom contains

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ASV with 0 hits filtering

I have two files as input here in picrust2 analysis: 1. seqs.fna 2. table.biom table.biom contains

6/26/23

ROHIT PATEL, Ricardo Rocha2

6/21/23

ASV cutoff for input files in picrust2

Hi Rohit, If I'm not wrong, for the Picrust the input should be an ASV table without

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ASV cutoff for input files in picrust2

Hi Rohit, If I'm not wrong, for the Picrust the input should be an ASV table without

6/21/23