Failed installation of q2-SCNIC plugin in qiime2-2019.10

Eman · November 18, 2019, 8:41pm

Hello,

I created a new environment for qiime2-2019.10 and named it qiime22-2019.10 to avoid any conflict when installing q2-SCNIC plugin (based on posted recommendations here
q2-SCNIC: A tool for making correlation networks, finding modules of observations and summarizing them
when I ran:
conda install -c lozuponelab q2-SCNIC

I got this error
Collecting package metadata: done
Solving environment: failed

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

q2-scnic -> q2-types=2018.11
q2-scnic -> qiime2=2018.11
q2-scnic -> scnic[version=’>=0.6.*’]

Current channels:

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.

#I searched similar topics and found this code
conda install -c lozuponelab -c conda-forge -c bioconda -c defaults --override-channels q2-SCNIC

That ended up to a new error:

Collecting package metadata: done
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:

q2-scnic
Use “conda search --info” to see the dependencies for each package.

These are info of installed qiime environment:
$qiime info
System versions
Python version: 3.6.7
QIIME 2 release: 2019.10
QIIME 2 version: 2019.10.0
q2cli version: 2019.10.0

Installed plugins
alignment: 2019.10.0
composition: 2019.10.0
cutadapt: 2019.10.0
dada2: 2019.10.0
deblur: 2019.10.0
demux: 2019.10.0
diversity: 2019.10.0
emperor: 2019.10.0
feature-classifier: 2019.10.0
feature-table: 2019.10.0
fragment-insertion: 2019.10.0
gneiss: 2019.10.0
longitudinal: 2019.10.0
metadata: 2019.10.0
phylogeny: 2019.10.0
quality-control: 2019.10.0
quality-filter: 2019.10.0
sample-classifier: 2019.10.0
taxa: 2019.10.0
types: 2019.10.0
vsearch: 2019.10.0

May you please explain these errors to me since I did not find any updates for installing q2-SCNIC in the new qiime release?

Thanks

jwdebelius · November 18, 2019, 8:52pm

Hi @Eman,

There may not be an update and you might want to run q2-SCNIC in 2018.11.

Best,
Justine

Eman · November 19, 2019, 3:14pm

I failed to install qiime2-2018.11 and got this error message:
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:

freetype=2.9.1
gstreamer=1.12.5
q2-gneiss=2018.11.0
Use “conda search --info” to see the dependencies for each package.

this conda info:
active environment : base
active env location : /home/eman/anaconda3
shell level : 1
user config file : /home/eman/.condarc
populated config files : /home/eman/.condarc
conda version : 4.6.14
conda-build version : 3.10.5
python version : 3.6.5.final.0
base environment : /home/eman/anaconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/linux-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/eman/anaconda3/pkgs
/home/eman/.conda/pkgs
envs directories : /home/eman/anaconda3/envs
/home/eman/.conda/envs
platform : linux-64
user-agent : conda/4.6.14 requests/2.18.4 CPython/3.6.5 Linux/4.15.0-70-generic ubuntu/16.04.6 glibc/2.23
UID:GID : 1000:1000
netrc file : None
offline mode : False

So, I do not know what to do next to figure it out?
Thanks

jwdebelius · November 19, 2019, 3:38pm

What commands did you use to install your qiime2-2018.11 enviroment? What kind of system are you using?

Best,
Justine

Eman · November 20, 2019, 3:35pm

I am just following the posted instructions:
wget https://data.qiime2.org/distro/core/qiime2-2018.11-py35-linux-conda.yml
conda env create -n qiime2-2018.11 --file qiime2-2018.11-py35-linux-conda.yml

as I am using Linux system (Ubuntu 16)

colinbrislawn · November 20, 2019, 4:25pm

With this new command, what errors are you getting?

Eman · November 20, 2019, 4:39pm

Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:

freetype=2.9.1
gstreamer=1.12.5
q2-gneiss=2018.11.0
Use “conda search --info” to see the dependencies for each package.

this conda info:
active environment : base
active env location : /home/eman/anaconda3
shell level : 1
user config file : /home/eman/.condarc
populated config files : /home/eman/.condarc
conda version : 4.6.14
conda-build version : 3.10.5
python version : 3.6.5.final.0
base environment : /home/eman/anaconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/linux-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/eman/anaconda3/pkgs
/home/eman/.conda/pkgs
envs directories : /home/eman/anaconda3/envs
/home/eman/.conda/envs
platform : linux-64
user-agent : conda/4.6.14 requests/2.18.4 CPython/3.6.5 Linux/4.15.0-70-generic ubuntu/16.04.6 glibc/2.23
UID:GID : 1000:1000
netrc file : None
offline mode : False

So, I do not know what to do next to figure it out?
Thanks
[/quote]

jwchen · November 20, 2019, 6:52pm

Hi @Eman,

I had the same issue and this is what I did:
Remove the failed environment, run the following command

conda clean -y --all

Then re-install QIIME2-2018.11.

Hope it helps.

Best,
Jiung-Wen

Eman · November 20, 2019, 9:48pm

I did and it did not work!

jwchen · November 21, 2019, 2:06am

I just check my laptop (macOS) and the Linux server and found it works for macOS but not for Linux (and I don’t know why ).
For the Linux server, I built a qiime2-2018.8 environment and successfully installed q2-SCNIC.

Eman · November 21, 2019, 1:14pm

I already have qiime2-2018.8 installed (once launched online), so I activated its environment and ran

conda update -n base -c defaults conda

then
conda install -c lozuponelab q2-SCNIC

get same error
Solving environment: failed

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

q2-scnic -> q2-types=2018.11
q2-scnic -> qiime2=2018.11
q2-scnic -> scnic[version=’>=0.6.*’]

Current channels:

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.

jwchen · November 21, 2019, 2:48pm

At least the environment issue is fixed
Now you may check the solution to the PackagesNotFoundError here:

Eman · November 21, 2019, 2:59pm

Great! it works with the posted command in the referred link:

conda install -c lozuponelab -c conda-forge -c bioconda -c defaults --override-channels q2-SCNIC

Thanks so much. Eman

Eman · November 21, 2019, 4:16pm

Since I am using qiime2-2019.10 now, so the created files can not be processed in qiime2-2018.8??
I ran
qiime SCNIC calculate-correlations \

--i-table table-1000.qza
--p-method sparcc
--o-correlation-table table-1000_correls.qza

I got

Traceback (most recent call last):
File "/home/eman/anaconda3/envs/qiime2-2018.8/bin/qiime", line 11, in
sys.exit(qiime())
File "/home/eman/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/home/eman/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/eman/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/eman/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/eman/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/eman/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/eman/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 244, in call
arguments, missing_in, verbose, quiet = self.handle_in_params(kwargs)
File "/home/eman/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 326, in handle_in_params
kwargs, fallback=cmd_fallback)
File "/home/eman/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/handlers.py", line 375, in get_value
artifact = qiime2.sdk.Result.load(path)
File "/home/eman/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/result.py", line 65, in load
archiver = archive.Archiver.load(filepath)
File "/home/eman/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 296, in load
cls._futuristic_archive_error(filepath, archive)
File "/home/eman/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 268, in _futuristic_archive_error
archive.version))
ValueError: table-no-mito-no-chlor-no-unass-l7-1000.qza was created by 'QIIME 2019.10.0'. The currently installed framework cannot interpret archive version '5'

So, I have to re-do everything in qiime2-2018.8 environment to use q2-SCNIC plugin!

jwchen · November 21, 2019, 4:39pm

Try this script in qiime2-2018.8 to get a new qza file. Make sure you modify the path in the script.

import pandas as pd
from qiime2 import Artifact

table = Artifact.load('path_of_your_qza_file')
df_table = table.view(pd.DataFrame)
new_table = Artifact.import_data('FeatureTable[Frequency]', df_table)
new_table.save('file_name_of_new_qza_file')

system · December 22, 2019, 10:39pm

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