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picrust-users

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Welcome! This group has been used for discussing and asking questions about PICRUSt and PICRUSt2.

We're now asking everyone to post these on the PICRUSt2 Github issues page so that we can consolidate things moving forwards. If you are asking for assistance troubleshooting then please post this as a bug report so that we can ask for all of the information that we'll need to help you.

If your question is about PICRUSt2 please first check the Frequently Asked Questions page and please search the previous messages (in the search bar above) before asking your question.

0 selected

Kirin_C, … Skyler Oliver14

Dec 3

Error in picrust2_pipeline.py command, possibly related to EPA-NG.

Hi everyone, I've been following along with this problem for a little while and did a little

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Error in picrust2_pipeline.py command, possibly related to EPA-NG.

Hi everyone, I've been following along with this problem for a little while and did a little

Dec 3

Nov 26

Moving discussion from Google groups to Github

Hello PICRUSt users! In order to try to simplify things moving forwards, we'll be asking everyone

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Moving discussion from Google groups to Github

Hello PICRUSt users! In order to try to simplify things moving forwards, we'll be asking everyone

Nov 26

Lasse Steffensen, Robyn Wright2

Nov 26

Discussion: Acceptable NSTI values in PICRUSt2

So sorry, I only just saw this and have just answered it on the Github. I'll just link to that

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Discussion: Acceptable NSTI values in PICRUSt2

So sorry, I only just saw this and have just answered it on the Github. I'll just link to that

Nov 26

Chieh-Chang Chen, Robyn Wright2

Nov 26

Running Picrust2 for large dataset

Hi there, Sorry for the delay. That does seem to be quite a lot of ASVs, as well as quite a lot of

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Running Picrust2 for large dataset

Hi there, Sorry for the delay. That does seem to be quite a lot of ASVs, as well as quite a lot of

Nov 26

小林陽子., Robyn Wright4

Oct 9

Error in run with a custom trait table

Hi Robyn, Thank you for your reply and for the very helpful advice! I also appreciate your decision

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Error in run with a custom trait table

Hi Robyn, Thank you for your reply and for the very helpful advice! I also appreciate your decision

Oct 9

Valentina Girardi

Oct 9

Why do path_abun_unstrat and path_cov_unstrat have different numbers of rows in PICRUSt2?

Hi everyone, I have a question about the pathway_pipeline.py outputs in PICRUSt2. After running the

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Why do path_abun_unstrat and path_cov_unstrat have different numbers of rows in PICRUSt2?

Hi everyone, I have a question about the pathway_pipeline.py outputs in PICRUSt2. After running the

Oct 9

jayos...@gmail.com, Robyn Wright4

Oct 2

pathway_pipeline.py key error

Hmm OK. Can you post your commands that you ran to get to this point? Was there a reason that you

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pathway_pipeline.py key error

Hmm OK. Can you post your commands that you ran to get to this point? Was there a reason that you

Oct 2

Andres Gerardo Fernandez Lehmann, Robyn Wright2

Oct 1

Error with - epa-ng

Hello, Apologies for my delayed reply. Can you please confirm whether you have followed the

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Error with - epa-ng

Hello, Apologies for my delayed reply. Can you please confirm whether you have followed the

Oct 1

youngtae won, Robyn Wright5

Jul 8

Inquiry Regarding PICRUST2 Input Data

It won't make a difference whether you run PICRUSt2 separately for each of the groups or together

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Inquiry Regarding PICRUST2 Input Data

It won't make a difference whether you run PICRUSt2 separately for each of the groups or together

Jul 8

David Liu, Robyn Wright2

Jul 7

Is there a way to do full length 16s functional analysis with picrust2

Hi David, You will be able to run PICRUSt2 exactly the same way with full-length 16S sequences as

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Is there a way to do full length 16s functional analysis with picrust2

Hi David, You will be able to run PICRUSt2 exactly the same way with full-length 16S sequences as

Jul 7

Kaitlin Ingram, … Robyn Wright9

May 20

PICRUSt2 for Mac M2

Hi again, I'm just coming back to this since updating PICRUSt2 on bioconda. I think that for Mac

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PICRUSt2 for Mac M2

Hi again, I'm just coming back to this since updating PICRUSt2 on bioconda. I think that for Mac

May 20

Rafael Ponce, Robyn Wright3

May 15

Missing reference files from the database

Hi there, I finally had a chance to properly look into this and it was an issue with the automatic

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Missing reference files from the database

Hi there, I finally had a chance to properly look into this and it was an issue with the automatic

May 15

matti.r...@gmail.com, … Robyn Wright7

May 14

Running Picrust 2.6.0 or later (Picrust2-SC db) from qiime2?

OK great. Just an FYI that if you used conda/mamba to install before today, some of the default

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Running Picrust 2.6.0 or later (Picrust2-SC db) from qiime2?

OK great. Just an FYI that if you used conda/mamba to install before today, some of the default

May 14

er qw, Robyn Wright2

May 12

picrust2 run error

Hi there, I think this could be an issue with your sequence names being only numbers, and one of the

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picrust2 run error

Hi there, I think this could be an issue with your sequence names being only numbers, and one of the

May 12

May 12

Rscript /home/tools/picrust2-2.6.2/picrust2/Rscripts/castor_nsti.R qiime_realsc/arc.tre /tmp/

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Rscript /home/tools/picrust2-2.6.2/picrust2/Rscripts/castor_nsti.R qiime_realsc/arc.tre /tmp/

May 12

LUCIA CABELLO ALEMAN, Robyn Wright2

Apr 28

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

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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

Apr 28

徐军明, Robyn Wright2

Apr 28

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

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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

Apr 28

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

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

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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 -

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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

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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

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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

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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

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