Plugin error from SCNIC: 'fastspar'

[Rashmi_Ira]

Hi,
@michael.shaffer @eandersk @nhuda6 @llenzi @thermokarst @cquin @arwqiime @mneranjan31 @kohei-108 and other QIIME2 users & developers...

I am working on q2-SCNIC tutorial shared by "@michael.shaffer q2-SCNIC: A tool for making correlation networks, finding modules of observations and summarizing them" & q2-SCNIC: Community Tutorial.

Currently, I am using QIIME2-2023.5 and was able to install q2-SCNIC using

@michael.shaffer

conda install -c conda-forge blas=1.1

then

**

pip install scnic

Next to install the plugin:

pip install git+https://github.com/lozuponelab/q2-SCNIC.git
qiime dev refresh-cache

**
&
Finally to see what functions are available, you can use:

qiime SCNIC --help

(it is working fine)

as command

@michael.shaffer

q2-SCNIC is available via bioconda so installing is easy. Just enter into your qiime 2 conda environment and use this command:

conda install -c lozuponelab q2-SCNIC

was not working and giving errors.

After installation of SCNIC using pip, I was able to perform importing of feature table

@michael.shaffer

qiime tools import \
  --input-path fake_data.biom \
  --type 'FeatureTable[Frequency]' \
  --input-format BIOMV210Format \
  --output-path fake_data.qza

and filtering of data

@michael.shaffer

To use the sparcc filter use this command:

qiime SCNIC sparcc-filter \
  --i-table fake_data.qza \
  --o-table-filtered fake_data-filtered.qza

but while running the next command for generating a correlation table

@michael.shaffer

qiime SCNIC calculate-correlations \
  --i-table fake_data-filtered.qza \
  --p-method sparcc \
  --o-correlation-table fake_correls.qza

It is giving an error:

Plugin error from SCNIC:

** [Errno 2] No such file or directory: 'fastspar'**

Debug info has been saved to /tmp/qiime2-q2cli-err-s1pz8hhr.log

I have also tried using
conda install -c bioconda -c conda-forge --override-channels fastspar

error: and loop loading for longer time

Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: / unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.

Then tried using:
**

conda install -q scnic

**
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... unsuccessful initial attempt using frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

• scnic

Current channels:

• main/linux-64
• main/noarch
• r/linux-64
• r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

Please suggest me how to proceed further? or is their another alternative to perform correlation network using qiime2???

Thanks in advance.

Best Regards,
Rashmi

[cherman2 (Chloe Herman)]

Hi @Rashmi_Ira,
Have you tried pip installing fastspar?
That worked for me previously. Hope that helps!

[Rashmi_Ira]

Hi @cherman2

Sorry for late response. I have used pip for scnic

@Rashmi_Ira

pip install scnic

But for

@cherman2

pip installing fastspar

No not yet. I'll try and let you know the status.