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picrust-users

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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.

Please note that after a number of spam messages, all messages now require approval. We try to do this as soon as possible, but this must be done manually. Please do not repost your message if you do not see it appear immediately.

0 selected

Kaitlin Ingram, … Kajal Kumari8

10:12 AM

PICRUSt2 for Mac M2

Functional prediction On Mon, 28 Apr 2025, 7:36 pm Robyn Wright, <roby...@gmail.com> wrote:

unread,

PICRUSt2 for Mac M2

Functional prediction On Mon, 28 Apr 2025, 7:36 pm Robyn Wright, <roby...@gmail.com> wrote:

10:12 AM

LUCIA CABELLO ALEMAN, Robyn Wright2

10:00 AM

outliers and different values between triplicates in pred_metagenome_unstrat file

Hi there, What are you using to open these files? That definitely does sound a bit weird! Can you use

unread,

outliers and different values between triplicates in pred_metagenome_unstrat file

Hi there, What are you using to open these files? That definitely does sound a bit weird! Can you use

10:00 AM

徐军明, Robyn Wright2

9:58 AM

How to use purchased KEGG

Hi there, Does the paid version of KEGG allow you to annotate genomes with it? If not, then no - you

unread,

How to use purchased KEGG

Hi there, Does the paid version of KEGG allow you to annotate genomes with it? If not, then no - you

9:58 AM

Zoë Williams, Robyn Wright4

Apr 14

Inconsistent output messages from picrust2

Hello Robyn, I wanted to follow up as I reran the data using the same command. Interestingly, KO was

unread,

Inconsistent output messages from picrust2

Hello Robyn, I wanted to follow up as I reran the data using the same command. Interestingly, KO was

Apr 14

Rafael Ponce, Robyn Wright2

Apr 9

Missing reference files from the database

Hi Rafael, I actually had the same issue and was trying to work out if it was just because I was

unread,

Missing reference files from the database

Hi Rafael, I actually had the same issue and was trying to work out if it was just because I was

Apr 9

Zoë Williams, Robyn Wright5

Apr 7

archaea output for v3-v4 sequencing?

Hello Robyn, These are great ideas for validating taxonomic classifications/picrust2 outputs that I

unread,

archaea output for v3-v4 sequencing?

Hello Robyn, These are great ideas for validating taxonomic classifications/picrust2 outputs that I

Apr 7

S. T., Robyn Wright2

Mar 28

COG, TIGRFAM "error - specified category is not one of the default categories."

Hi there, You're correct, COG and TIGRFAM are not available in the latest version - I've used

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COG, TIGRFAM "error - specified category is not one of the default categories."

Hi there, You're correct, COG and TIGRFAM are not available in the latest version - I've used

Mar 28

Anandi Batabyal, … Kajal Kumari10

Mar 28

Metagenome prediction using ggpicrust2

Help On Thu, 27 Mar 2025, 11:00 pm Robyn Wright, <roby...@gmail.com> wrote: I already said -

unread,

Metagenome prediction using ggpicrust2

Help On Thu, 27 Mar 2025, 11:00 pm Robyn Wright, <roby...@gmail.com> wrote: I already said -

Mar 28

TY H, Robyn Wright6

Mar 27

how I change the ko database

Thanks for clarifying. As this is a single function and not an entire database of organisms, I'd

unread,

how I change the ko database

Thanks for clarifying. As this is a single function and not an entire database of organisms, I'd

Mar 27

Subhrangshu Mandal, Robyn Wright12

Mar 25

Guide me to generate .fna and .biom file

Hi there, Unfortunately there isn't really any way around this. This means that there was nothing

unread,

Guide me to generate .fna and .biom file

Hi there, Unfortunately there isn't really any way around this. This means that there was nothing

Mar 25

Anandi Batabyal, Robyn Wright3

Mar 25

PICRUST2 output

Thanks so much! I appreciate it. Best, Anandi On Thursday, 27 February 2025 at 08:13:04 UTC-5 roby...

unread,

PICRUST2 output

Thanks so much! I appreciate it. Best, Anandi On Thursday, 27 February 2025 at 08:13:04 UTC-5 roby...

Mar 25

Ivanova Stasja, Robyn Wright3

Mar 18

Picrust2 Output clarification and ggpicrust2 Input

Thank you so much for the clarification, I got it! All the best! вт, 18 мар. 2025 г. в 17:06, Robyn

unread,

Picrust2 Output clarification and ggpicrust2 Input

Thank you so much for the clarification, I got it! All the best! вт, 18 мар. 2025 г. в 17:06, Robyn

Mar 18

Ian Blixt, … Robyn Wright6

Feb 25

pplacer or similar placement issue

Hi, Could you give details on how you installed PICRUSt2 please? Thanks, Robyn On Tuesday, 25

unread,

pplacer or similar placement issue

Hi, Could you give details on how you installed PICRUSt2 please? Thanks, Robyn On Tuesday, 25

Feb 25

Amal Arifi, Robyn Wright2

Feb 25

Error in qiime2 picrust2 plug-in

Hi there, Could you give some more information on where you're running this - how much memory do

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Error in qiime2 picrust2 plug-in

Hi there, Could you give some more information on where you're running this - how much memory do

Feb 25

SY, Robyn Wright2

Feb 21

Default Mapfile of PICRUSt2 New Version

Hi there, Thank you so much for noticing this and pointing it out. I've now replaced the files in

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Default Mapfile of PICRUSt2 New Version

Hi there, Thank you so much for noticing this and pointing it out. I've now replaced the files in

Feb 21

Dimitrios-Marinos Karadedos, Robyn Wright2

Feb 18

Error running pipcrust2_pipeline.py

Hi there, Could you please attach (as a text file, ideally) the full output that you get? And can you

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Error running pipcrust2_pipeline.py

Hi there, Could you please attach (as a text file, ideally) the full output that you get? And can you

Feb 18

Jay, Robyn Wright2

Feb 18

Assistance required converting Mothur-generated BIOM File for PICRUSt2 analysis

Hi Jay, I'm actually not familiar with the biom-validate command, but you don't mention

unread,

Assistance required converting Mothur-generated BIOM File for PICRUSt2 analysis

Hi Jay, I'm actually not familiar with the biom-validate command, but you don't mention

Feb 18

Misbah Tubassam, … Robyn Wright29

Feb 18

Picrust2 Installation in Mac M1

I am so glad that this (finally) worked for you, and thanks for sharing the steps that worked -

unread,

Picrust2 Installation in Mac M1

I am so glad that this (finally) worked for you, and thanks for sharing the steps that worked -

Feb 18

Subhrangshu Mandal, Robyn Wright2

Feb 10

Converting Ion Torrent Amplicon Data (V3-V4) to PICRUSt2-Compatible Files (.fna and .biom)

Hi there, You'll need to process your data using a regular amplicon sequencing workflow first -

unread,

Converting Ion Torrent Amplicon Data (V3-V4) to PICRUSt2-Compatible Files (.fna and .biom)

Hi there, You'll need to process your data using a regular amplicon sequencing workflow first -

Feb 10

Chao-Jui Chang, Robyn Wright2

Feb 10

Installation issue for version 2.6.0

Hi Chao-Jui, The command picrust2_pipeline_split.py is one that I was initially using for the new

unread,

Installation issue for version 2.6.0

Hi Chao-Jui, The command picrust2_pipeline_split.py is one that I was initially using for the new

Feb 10

Rebecca Brittain, … Peter Chimaobi3

Jan 22

picrust2 - unplaced ASV list

Hi, I don't know if this relates to your question but when I run picrust2 with --verbose flag, it

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picrust2 - unplaced ASV list

Hi, I don't know if this relates to your question but when I run picrust2 with --verbose flag, it

Jan 22

Artur Zaduryan, Karla Camacho Mendez2

Jan 22

epa-ng command error without any details...

Hi! in my workflow I had the same! However, I have a external Ram integrated in my laptop. When I

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epa-ng command error without any details...

Hi! in my workflow I had the same! However, I have a external Ram integrated in my laptop. When I

Jan 22

Sara Beier, … Sara Beier5

Jan 22

hidden state predictions with custom tree

I meanwhile run the code with the --verbose option (picrust2-2.3.0_b versus picrust-2.5.0 ). The

unread,

hidden state predictions with custom tree

I meanwhile run the code with the --verbose option (picrust2-2.3.0_b versus picrust-2.5.0 ). The

Jan 22

andrea firrincieli, Robyn Wright2

Jan 13

PICRUSt2 v2.6.0 GTDB

Hi there, If you used the same picrust2_pipeline.py command then PICRUSt2 will still run with the

unread,

PICRUSt2 v2.6.0 GTDB

Hi there, If you used the same picrust2_pipeline.py command then PICRUSt2 will still run with the

Jan 13

Subhrangshu Mandal, Robyn Wright2

Jan 6

Guidance on Choosing the Appropriate PICRUSt2 Version

Hi there, To my understanding, ggpicrust2 is a package made by another group that is for analysing

unread,

Guidance on Choosing the Appropriate PICRUSt2 Version

Hi there, To my understanding, ggpicrust2 is a package made by another group that is for analysing

Jan 6

Dewey Ryn, Robyn Wright2

Jan 6

how to work on ARM64 platform？

Hi there, I don't have a Linux ARM server that I can test with and am certainly not an expert on

unread,

how to work on ARM64 platform？

Hi there, I don't have a Linux ARM server that I can test with and am certainly not an expert on

Jan 6

Robyn Wright, Misbah Tubassam2

Jan 6

Re: File name too long with --per_sequence_contrib

Hey Robyn, I hope you are doing great. I am trying to install PICRUST2 in my Macbook M1 with the code

unread,

Re: File name too long with --per_sequence_contrib

Hey Robyn, I hope you are doing great. I am trying to install PICRUST2 in my Macbook M1 with the code

Jan 6

chasanmirza wibisono, Robyn Wright2

12/16/24

Confusing About The Result of Pathway Prediction

Hi Chasan, I wouldn't be too worried about that personally - in one of the KEGG papers, they say

unread,

Confusing About The Result of Pathway Prediction

Hi Chasan, I wouldn't be too worried about that personally - in one of the KEGG papers, they say

12/16/24

chasanmirza wibisono

12/9/24

Confusing about The Heatmap Result

Hi there. I am new here I just confusing about the heatmap KEGG pathway prediction My sample is

unread,

Confusing about The Heatmap Result

Hi there. I am new here I just confusing about the heatmap KEGG pathway prediction My sample is

12/9/24

Chao-Jui Chang, Robyn Wright4

11/13/24

Question on path_abun_unstrat

That's not currently an option with the default files, but I believe that if you made a mapping

unread,

Question on path_abun_unstrat

That's not currently an option with the default files, but I believe that if you made a mapping

11/13/24

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