Hi, when will be any updates on q2-scnic for the latest qiime2 version? Thanks
A post was split to a new topic: Canât install q2-SCNIC
Hello, I am following the q2-SCNIC pipeline in QIIME2 core- 2018.8 and am on the "Calculating correlations and making your network" step.
Everytime I try to run qiime SCNIC calculate-correlations --i-table test-filtered.qza --p-method sparcc --o-correlation-table fake_correls.qza
I get an error saying:
Plugin error from SCNIC:
[Errno 2] No such file or directory: 'fastspar'
Debug info has been saved to /tmp/qiime2-q2cli-err-iy4g0idr.log
Things I have tried: reinstalling everything:
conda install -c conda-forge blas=1.1
conda update -n base -c defaults conda
conda install -c lozuponelab q2-SCNIC
pip install scnic
conda install fastspar
conda update fastspar
At some point I also tried,
conda config --add channels conda-forge
conda config --add channels defaults
Nothing worked. I then tried running Spearman correlation thinking it was just an issue with fastspar and I got:
Plugin error from SCNIC:
calculate_correlations() got an unexpected keyword argument 'p_adjustment_method'
Debug info has been saved to /tmp/qiime2-q2cli-err-xd2b8aj_.log
So I think it's an issue with my SCNIC.
Any feedback would be greatly appreciated.
I was following your instructions to add q2-SCNIC to q2-2021.2
conda install -c conda-forge blas=1.1
It causes a downgrade of blas; is this necessary, or should it be avoided?
The following packages will be DOWNGRADED:
blas 2.17-openblas â 1.1-openblas
Best,
Dear All,
I am trying to use q2-SCNIC to generate the correlation network using the genus level table in my microbiome data. I have generated ânetwork-module.qzaâ file which could be imported to cytoscape according to the tutorial. I am wondering whether is it possible to directly import a .qza format network file to cytoscape for the visualization? If it is not possible import directly, could you please suggest me a possible way to import the âmodule-network.qzaâ file generated by q2-SCNIC to cytoscape? Any help is greatly appreciated!
Thanks in advance!
Madhawa
thank you for your great tutorial. but how we can identify hub nodes in qiime2 if we don't want to use WGCNA?
Hello @mneranjan31
You can use qiime tools extract
command.
# The directory that youâre extracting to must already exist.
mkdir extracted-network/
qiime tools extract --input-path network-module.qza --output-path extracted-network/
Then, you can find network.gml in extracted-network/{random string}/data/
.
You load this file into Cytoscape.
Kohei
Hi @kohei-108 ,
Thank you for your kind help with the command. It is very helpful for me.!!
Best Regards,
Madhawa
An off-topic reply has been split into a new topic: I am wondering How you import the biom file including the (spp or the genus level) as my .biom file contains only the sequence representing every OTU
Please keep replies on-topic in the future.