PICRUSt Analysis

#1

Hie guys am trying thinking of doing predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. I’m hoping to do this using PICRUSt however during taxonomic classification i used SILVA as my reference database instead of Greengenes does this matter since PICRUSt seems to be preferring data from Greengenes?

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(Justine) #2

Hi @Tinaye,

No your taxonomic reference database doesn’t matter, because PICRUSt 2 uses it’s own reference tree. I’d recommend reading the PICRUSt tutorial because it better explains better than I can.

Best,
Justine

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#3

Thanks hey however I,ve tried the q2-PICRUSt plugin installation and during the process i encounter this error

(qiime2-2018.11) MacBooks-MBP:picrust2-2.0.3-b macbook$ conda update -n qiime2-2018.11 -f picrust2-env.yaml

WARNING: The --force flag will be removed in a future conda release.
See ‘conda update --help’ for details about the --force-reinstall
and --clobber flags.

PackageNotInstalledError: Package is not installed in prefix.
prefix: /miniconda3/envs/qiime2-2018.11
package name: picrust2-env.yaml

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(Jianjian Hou) #4

I think you should follow the q2-picrust2 install guide.
https://library.qiime2.org/plugins/q2-picrust2/13/

wget https://github.com/picrust/picrust2/releases/download/v2.0.3-b/picrust2-2.0.3-b.zip
unzip picrust2-2.0.3-b.zip
cd picrust2-2.0.3-b
conda-env update -n qiime2-2019.1 -f picrust2-env.yaml
pip install --editable .

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(Justine) #5

If you’re using qiime2.2018.11, you should use the name qiime2-2018.11 instead of qiime2-2019.1.

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#6

Yes i did, actually i changed my qiime to 2019.1 but i still get the same error. From what i can tell the problem might be my picrust2-env.yaml is a read only file.

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(Justine) #7

For that, you could maybe try re-downloading the file in a directory where you have re-write permissions, or modifying the permission on the file?

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#8

Hey thanks that’s the exact install guide am following which is giving me multiple errors. For example the conda-env command is not a command.

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(Gavin Douglas) #9

Hi @Tinaye,

What version of conda are you running? Does using “conda env” instead of “conda-env” make a difference?

Gavin

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