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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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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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
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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If you're using qiime2.2018.11, you should use the name qiime2-2018.11 instead of qiime2-2019.1.
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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.
Hi @Tinaye,
What version of conda are you running? Does using "conda env" instead of "conda-env" make a difference?
Gavin
An off-topic reply has been split into a new topic: PICRUSt Unsatisfiable Error
Please keep replies on-topic in the future.
Hi @Tinaye
Did u get it to work? I wonder if you had the same issue that I had. We were working in what are called as singularity containers. And because this is a plugin we were told to the following (as boldfaced) before the actual script and it worked.
module load singularity/3
export TZ='Pacific/Auckland'
*/workspace/hraegb/singularity/qiime-2019.7-picrust2.sif picrust2 full-pipeline *
--i-table $FILTER/table-dada2.qza
--i-seq $FILTER/rep-seqs-dada2.qza
--output-dir $WORKING/$PICR2/pic
--o-ko-metagenome $PICR2/KO
--o-ec-metagenome $PICR2/EC
--o-pathway-abundance $PICR2/PA
--p-threads 1
--p-hsp-method mp
--p-max-nsti 2
--verbose
regards
Seta