Error about picrust2

[gavinmdouglas]

Hi @ricmedveterinario ,

My guess is that a different version of pandas is installed than specified in the PICRUSt2 installation YAML. How did you install PICRUSt2 and what version is it?

You can see the versions of the packages installed in your currently activated environment with:
conda list

Depending on what version of PICRUSt2 is installed you probably need pandas version 0.22.0.

[ricmedveterinario]

Hi gavinmdouglas

We are installing and trying to make the program run on its own server,

We were then able to fix by installing the appropriate panda version.

With a virtualenv library, where we installed the required version of the pandas library, isolating the picrust2 installation,

However we had no further problem as follows:

"4686 of 4686 sequence ids overlap between input table and FASTA.

Error running this command:
hsp.py --tree picrust2_out_pipeline / out.tre --output picrust2_out_pipeline / EC_predicted.tsv --observed_trait_table /data/apps/picrust/2.1.0-b/python3.5.1/virtualenv/lib/python3.5/site-packages /PICRUSt2-2.1.0b0-py3.5.egg/picrust2/default_files/prokaryotic/ec.txt.gz --hsp_method mp --processes 4 --seed 100

STDOUT of failed command: "

How could we solve it? since we are putting the program to run for a whole university.

Thank you.

[gavinmdouglas]

Hi @ricmedveterinario ,

First I would recommend installing the latest version of PICRUSt2 (v2.1.2-b), which should allow this error message to be printed correctly. Alternatively you could try running the command with 1 core to see the error since I believe the reason why no error message is being printed is that it happened while the command was parallelized. If that allows you to see the error message, please post it here.

The tool was designed to be installed with conda so that all correct versions of the pre-requisites would be installed. If you can't use conda for how you're installing the tool you can take a look at the "picrust2-env.yaml" file in the repo of the version you're using to see the versions of all required pre-requisites. If the reported error has to do with a particular python package I would make sure the installed version matches what is listed in the YAML.

[ricmedveterinario]

Thank you gavinmdouglas,

We will be checking everything and soon we will report if everything went well,

Soon I will bring news,

[gavinmdouglas]

Closing due to inactivity.