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?
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.
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.
package name: picrust2-env.yaml
I think you should follow the q2-picrust2 install guide.
conda-env update -n qiime2-2019.1 -f picrust2-env.yaml
pip install --editable .
If you’re using qiime2.2018.11, you should use the name
qiime2-2018.11 instead of
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.
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?
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.
What version of conda are you running? Does using “conda env” instead of “conda-env” make a difference?
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