# About q2-SCNIC installation
**URL:** https://forum.qiime2.org/t/about-q2-scnic-installation/20245
**Category:** Library Support
**Created:** [July 19, 2021, 11:03pm UTC](https://forum.qiime2.org/t/about-q2-scnic-installation/20245 "2021-07-19T23:03:46Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@WeedCentipede](https://forum.qiime2.org/u/WeedCentipede)
#### Post date: [July 19, 2021, 11:03pm UTC](https://forum.qiime2.org/t/about-q2-scnic-installation/20245/1 "2021-07-19T23:03:46Z")
Hello there!
I'm trying to figure out how to install and run SCNIC but facing my inhability to do it, I feel like a Gordon Ramsay's 🥪.
Lately I've reproduced errors ranging from the ones previously reported in [q2-SCNIC Correlations calculation #error plugin DataFrame to\_dense](https://forum.qiime2.org/t/q2-scnic-correlations-calculation-error-plugin-dataframe-to-dense/18460) and [q2 scnic fails in calculating correlations](https://forum.qiime2.org/t/q2-scnic-fails-in-calculating-correlations/18932) which apparently are due to the q2 environment version (mainly 2021.4, 2020.8, 2020.11); to other errors associated with the conda channel, pip installation, missing libraries (networkx and/or r-pillar=1.2.2 in q2-2018.8), no longer supported and conflicted envs (q2-2018.11), etc (I've lost count of all the errors so far).
My question: is this plugin still functional and ready to use? and if it is under what conditions needs to be installed in order to run properly?
Cheers,
Luis Alfonso.
PD, I know this topic kinda resurfaces every two months so if it's redundant please don't accept it.
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### Author:  [@kthurimella](https://forum.qiime2.org/u/kthurimella)
#### Post date: [July 20, 2021, 4:22pm UTC](https://forum.qiime2.org/t/about-q2-scnic-installation/20245/2 "2021-07-20T16:22:24Z")
Hey Luis, did you have any issues installing the plugin using these commands: [https://library.qiime2.org/plugins/q2-scnic/11/](https://library.qiime2.org/plugins/q2-scnic/11/)?
---
### Author:  [@WeedCentipede](https://forum.qiime2.org/u/WeedCentipede)
#### Post date: [July 20, 2021, 11:35pm UTC](https://forum.qiime2.org/t/about-q2-scnic-installation/20245/3 "2021-07-20T23:35:41Z")
Hey Kumar,
Following the link's commands, installing with pip, in qiime 2021.2 (and other recent qiime2 versions), python 3.6.13, I get the following error:
(qiime2-20212) [larteag7@apolo workdir-feb2021] pip install --user scnic
Requirement already satisfied: scnic in /home/larteag7/.conda/envs/qiime2-20212/lib/python3.6/site-packages (0.6.2)
Requirement already satisfied: networkx\>=2 in /home/larteag7/.conda/envs/qiime2-20212/lib/python3.6/site-packages (from scnic) (2.5)
(qiime2-20212) [larteag7@apolo workdir-feb2021]$ pip install git+https://github.com/lozuponelab/q2-SCNIC.git
Collecting git+https://github.com/lozuponelab/q2-SCNIC.git
Cloning [GitHub - lozuponelab/q2-SCNIC: A QIIME2 plugin for running SCNIC](https://github.com/lozuponelab/q2-SCNIC.git) to /tmp/pip-req-build-sjg3ewpk
Running command git clone -q [GitHub - lozuponelab/q2-SCNIC: A QIIME2 plugin for running SCNIC](https://github.com/lozuponelab/q2-SCNIC.git) /tmp/pip-req-build-sjg3ewpk
Building wheels for collected packages: q2-SCNIC
Building wheel for q2-SCNIC (setup.py) ... done
Created wheel for q2-SCNIC: filename=q2\_SCNIC-2020.10+4.gf8566e7-py3-none-any.whl size=13659 sha256=fc8d940bcab83bfe52d67cefaeffd6b5b0528c84f9f02a27f21ba67c861c3447
Stored in directory: /tmp/pip-ephem-wheel-cache-\_sk\_h2f1/wheels/64/7b/3c/5bcf3c4eb19280ce7539e810efd388ff14d07e9c5283f87c24
Successfully built q2-SCNIC
Installing collected packages: q2-SCNIC
Attempting uninstall: q2-SCNIC
Found existing installation: q2-SCNIC 2018.8.0+20.g07ffa4a
Uninstalling q2-SCNIC-2018.8.0+20.g07ffa4a:
Successfully uninstalled q2-SCNIC-2018.8.0+20.g07ffa4a
Successfully installed q2-SCNIC-2020.10+4.gf8566e7
...
(qiime2-20212) [larteag7@apolo workdir-feb2021]$ qiime SCNIC calculate-correlations --i-table fake-data-filtered.qza --p-method sparcc --o-correlation-table fake-correls.qza
Plugin error from SCNIC:
'DataFrame' object has no attribute 'to\_dense'
Debug info has been saved to /tmp/qiime2-q2cli-err-0dzoplyr.log
(qiime2-20212) [larteag7@apolo workdir-feb2021]$ cat /tmp/qiime2-q2cli-err-0dzoplyr.log
Correlating with sparcc
Traceback (most recent call last):
File "/home/larteag7/.conda/envs/qiime2-20212/lib/python3.6/site-packages/q2cli/commands.py", line 329, in **call**
results = action(\*\*arguments)
File "", line 2, in calculate\_correlations
File "/home/larteag7/.conda/envs/qiime2-20212/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound\_callable
output\_types, provenance)
File "/home/larteag7/.conda/envs/qiime2-20212/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in _callable\_executor_
output\_views = self.\_callable(\*\*view\_args)
File "/home/larteag7/.conda/envs/qiime2-20212/lib/python3.6/site-packages/q2\_SCNIC/\_SCNIC\_methods.py", line 29, in calculate\_correlations
correls = ca.fastspar\_correlation(table, verbose=True, nprocs=n\_procs)
File "/home/larteag7/.conda/envs/qiime2-20212/lib/python3.6/site-packages/SCNIC/correlation\_analysis.py", line 77, in fastspar\_correlation
table.to\_dataframe().to\_dense().to\_csv(path.join(temp, 'otu\_table.tsv'), sep='\t', index\_label='#OTU ID')
File "/home/larteag7/.conda/envs/qiime2-20212/lib/python3.6/site-packages/pandas/core/generic.py", line 5141, in **getattr**
return object. **getattribute** (self, name)
AttributeError: 'DataFrame' object has no attribute 'to\_dense'
As someone mentioned before, in the same step if you use a different method, it works.
(qiime2-20212) [larteag7@apolo workdir-feb2021]$ qiime SCNIC calculate-correlations --i-table fake-data-filtered.qza --p-method pearson --o-correlation-table fake-correls.qza
Saved PairwiseFeatureData to: fake-correls.qza
I read somewhere than in an 2018 version of qiime it might work so, following link's commands installing with pip, in qiime 2018.8, python 3.5.5, I get the following error:
(qiime2-20188) [larteag7@apolo workdir-feb2021] pip install --user scnic
Collecting scnic
Collecting networkx\>=2 (from scnic)
Using cached [https://files.pythonhosted.org/packages/41/8f/dd6a8e85946def36e4f2c69c84219af0fa5e832b018c970e92f2ad337e45/networkx-2.4-py3-none-any.whl](https://files.pythonhosted.org/packages/41/8f/dd6a8e85946def36e4f2c69c84219af0fa5e832b018c970e92f2ad337e45/networkx-2.4-py3-none-any.whl)
Installing collected packages: networkx, scnic
Successfully installed networkx-2.4 scnic-0.6.2
(qiime2-20188) [larteag7@apolo workdir-feb2021] pip install git+https://github.com/lozuponelab/q2-SCNIC.git
Collecting git+https://github.com/lozuponelab/q2-SCNIC.git
Cloning [GitHub - lozuponelab/q2-SCNIC: A QIIME2 plugin for running SCNIC](https://github.com/lozuponelab/q2-SCNIC.git) to /tmp/pip-req-build-ed9vwtrj
Requirement already satisfied (use --upgrade to upgrade): q2-SCNIC==2020.10+4.gf8566e7 from git+https://github.com/lozuponelab/q2-SCNIC.git in /home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages
Building wheels for collected packages: q2-SCNIC
Running setup.py bdist\_wheel for q2-SCNIC ... done
Stored in directory: /tmp/pip-ephem-wheel-cache-4ufgz68z/wheels/ad/4f/90/efd772f34ca8f61d2990b841f051aaf9ecdb816e01512ae3a1
Successfully built q2-SCNIC
(qiime2-20188) [larteag7@apolo workdir-feb2021]$ qiime dev refresh-cache
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
File "/home/larteag7/.conda/envs/qiime2-20188/bin/qiime", line 11, in
sys.exit(qiime())
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/click/core.py", line 722, in **call**
return self.main(\*args, \*\*kwargs)
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return \_process\_result(sub\_ctx.command.invoke(sub\_ctx))
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return \_process\_result(sub\_ctx.command.invoke(sub\_ctx))
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, \*\*ctx.params)
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(\*args, \*\*kwargs)
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/q2cli/dev.py", line 27, in refresh\_cache
import q2cli.cache
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/q2cli/cache.py", line 301, in
CACHE = DeploymentCache()
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/q2cli/cache.py", line 61, in **init**
self.\_state = self.\_get\_cached\_state(refresh=refresh)
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/q2cli/cache.py", line 107, in \_get\_cached\_state
self.\_cache\_current\_state(current\_requirements)
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/q2cli/cache.py", line 200, in \_cache\_current\_state
state = self.\_get\_current\_state()
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/q2cli/cache.py", line 238, in \_get\_current\_state
plugin\_manager = qiime2.sdk.PluginManager()
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/qiime2/sdk/plugin\_manager.py", line 44, in **new**
self.\_init()
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/qiime2/sdk/plugin\_manager.py", line 59, in \_init
plugin = entry\_point.load()
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/pkg\_resources/ **init**.py", line 2325, in load
return self.resolve()
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/pkg\_resources/ **init**.py", line 2331, in resolve
module = **import** (self.module\_name, fromlist=[' **name**'], level=0)
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/q2\_SCNIC/plugin\_setup.py", line 7, in
from q2\_SCNIC.\_format import GraphModelingLanguageFormat, GraphModelingLanguageDirectoryFormat, PairwiseFeatureDataFormat,
File "/home/larteag7/.conda/envs/qiime2-20188/lib/python3.5/site-packages/q2\_SCNIC/\_format.py", line 3, in
import networkx as nx
ImportError: No module named 'networkx'
Let me know what you think,
Luis.
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### Author:  [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [July 21, 2021, 2:19pm UTC](https://forum.qiime2.org/t/about-q2-scnic-installation/20245/4 "2021-07-21T14:19:36Z")
Hi!
I collected all above mentioned errors while trying to work with SCNIC or q2-SCNIC.
The problem is that 'to\_dense' function was deprecated in version 1.0, so you need to downgrade to pandas 0.25
Do not use conda to downgrade since it will mess with dependencies.
For me worked:
`pip install pandas==0.25`
PS. Do not forget to upgrade pandas back to previous version since you may encounter some errors in other plugins,or install a separate qiime2 version that will be used only for SCNIC
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### Author:  [@WeedCentipede](https://forum.qiime2.org/u/WeedCentipede)
#### Post date: [July 22, 2021, 8:40pm UTC](https://forum.qiime2.org/t/about-q2-scnic-installation/20245/5 "2021-07-22T20:40:15Z")
Hi Timur,
Sorry for the late answer!
It worked, then it failed due to fastspar but after a conda installation (following cmd)
> conda install -c bioconda -c conda-forge --override-channels fastspar
I was finally able to run scnic,
Thank you so much,
Cheers,
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### Author:  [@cherman2](https://forum.qiime2.org/u/cherman2)
#### Post date: [July 26, 2023, 4:51pm UTC](https://forum.qiime2.org/t/about-q2-scnic-installation/20245/6 "2023-07-26T16:51:52Z")
2 off-topic replies have been split into a new topic: [q2-scnic not compatible with 2023.5 feature table](https://forum.qiime2.org/t/q2-scnic-not-compatible-with-2023-5-feature-table/27212)
Please keep replies on-topic in the future.