Picrust2 plugin in QIIME2-2019.1

[tar...@ucsb.edu]

Hi Gavin - Is the Picrust2 plugin not compatible with the newer version of Qiime2-2019.1? When I updated Q2, I lost the Picrust2 plugin functionality. 

Thank you so much! -Taruna

[Gavin Douglas]

Hi Taruna,

I haven't tested out the plugin with the new QIIME2 release yet, but I will this weekend and will get back to you.

Just to clarify - did you re-install the q2-picrust2 plugin in the new qiime2-2019.1 environment and it didn't work?

Best,

Gavin

On 2019-02-08 5:24 p.m., tar...@ucsb.edu wrote:

Hi Gavin - Is the Picrust2 plugin not compatible with the newer version of Qiime2-2019.1? When I updated Q2, I lost the Picrust2 plugin functionality. 

Thank you so much! -Taruna

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[Taruna Schuelke]

Hi Gavin - thank you for checking. I did reinstall the plugin, but the newer Qiime2 version wouldn't recognize the picrust command. 

Taruna

[Gavin Douglas]

Hi Taruna,

When you installed PICRUSt2 did you swap out “qiime2-2018.11” with "qiime2-2019.1”?

E.g. in this command:

conda-env update -n qiime2-2018.11 -f picrust2-env.yaml

I was just able to install the plugin in qiime2-2019.01 so I’m not sure what else could be the problem.

Gavin

[Taruna Schuelke]

Hi Gavin - I did not run the update command so it makes sense why Picrust2 wasn't working with the newer Qiime2 version. May I please request a modification to the installation instructions? If you don't mind, can you please post this update command in the instructions too? I just learned how to install things with conda and it did not occur to me that I should just update the plugin. I am sure there are others who ran into the same problem but knowing that you can update the conda env would be helpful. 

Thank you very much again for looking into this!

Taruna 

[Gavin Douglas]

Hi Taruna,

The update command is already part of the install instructions here: https://library.qiime2.org/plugins/q2-picrust2/13/. Were you referring to somewhere else?

Best,

Gavin

[Taruna Schuelke]

Ah okay! I was using the instructions on Github. 

[kkalya...@gmail.com]

Hello,
I have installed picrust2 from qiime2 library plugin itself. But still,
When I run the following command-
qiime picrust2 custom-tree-pipeline --i-table table-cr-99.qza
–i-tree tutorial_placed_out/tree.qza
–output-dir q2-picrust2_output
–p-threads 1 --p-hsp-method pic
–p-max-nsti 2
I get the following error-
Error: No such command “picrust2”.
I followed the commands for picrust2 analysis from q2 picrust2 Tutorial.
Can someone guide as to why this problem must have occured.
Kindly help with this

[Taruna Schuelke]

Hi - is your Qiime environment activated? 

--

[Gavin Douglas]

Hi there,

Did you run into any errors when installing q2-picrust2 or picrust2? Did you get an error about the command “conda-env” not being found by chance?

Gavin

[kkalya...@gmail.com]

Yes it is.I could even install the picrust without any hassles and even run the first command properly.
qiime fragment-insertion sepp --i-representative-sequences rep-seqs-cr-99.qza \
                              --p-threads 1 --i-reference-alignment reference.fna.qza \
                              --i-reference-phylogeny reference.tre.qza \
                              --output-dir tutorial_placed_out

I am facing an issue for the command after that. i.e.qiime picrust2 custom-tree-pipeline --i-table table-cr-99.qza \
                                    --i-tree tutorial_placed_out/tree.qza \
                                    --output-dir q2-picrust2_output \
                                    --p-threads 1 --p-hsp-method pic \
                                    --p-max-nsti 2

Thank you.

Regards

[Gavin Douglas]

That first command is another QIIME2 plugin so I believe something must have gone wrong during the installation of PICRUSt2 or q2-picrust2. Could you try re-installing the plugin in a fresh QIIME2 environment and check if any errors occur during the installation?

Best,

Gavin

[kkalya...@gmail.com]

Ok. Thanks.
I have done the installation process from- https://library.qiime2.org/plugins/q2-picrust2/13/
It would be be great if I could get some help with the installation commands in case  the issue is arising because of installation.

[kkalya...@gmail.com]

Hello,
I would again need help.
I am getting the following error-
hsp.py -i 16S -t /tmp/tmptcr_egf1/placed_seqs.tre -p 1 -n -o /tmp/tmptcr_egf1/picrust2_out/16S_predicted -m pic
For the following command-

qiime picrust2 custom-tree-pipeline --i-table table-cr-99.qza \
                                    --i-tree tutorial_placed_out/tree.qza \
                                    --output-dir q2-picrust2_output \
                                    --p-threads 1 --p-hsp-method pic \
                                    --p-max-nsti 2

Kindly help to resolve the error.
Thank you.
Regards

[Gavin Douglas]

Would you mind sending me your input files privately and I can help you troubleshoot?

Thanks,

Gavin