SCNIC, calculate-correlations fastspar not found

Hi All,

I have been trying to run SCNIC on some data, I installed it using the following link GitHub - shafferm/q2-SCNIC: A QIIME2 plugin for running SCNIC .

the sparcc-filter ran without error and i ran put the output into calculate-correlations method but i got the following error when ran with the --verbose option

Correlating with sparcc
Traceback (most recent call last):
File “/opt/conda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</opt/conda/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-873>”, line 2, in calculate_correlations
File “/opt/conda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/opt/conda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/opt/conda/envs/qiime2-2019.10/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 “/opt/conda/envs/qiime2-2019.10/lib/python3.6/site-packages/SCNIC/correlation_analysis.py”, line 83, in fastspar_correlation
path.join(temp, ‘covar_table.tsv’), stdout, nprocs)
File “/opt/conda/envs/qiime2-2019.10/lib/python3.6/site-packages/SCNIC/correlation_analysis.py”, line 71, in run_fastspar
covar_table_loc, ‘-t’, str(nprocs)], stdout=stdout, check=True)
File “/opt/conda/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 403, in run
with Popen(*popenargs, **kwargs) as process:
File “/opt/conda/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 709, in init
restore_signals, start_new_session)
File “/opt/conda/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 1344, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: ‘fastspar’: ‘fastspar’

Plugin error from SCNIC:

[Errno 2] No such file or directory: ‘fastspar’: ‘fastspar’

Debug info has been saved to /tmp/qiime2-q2cli-err-05bthxpa.log

I have tried reinstalling the plugin but it didnt fix the error

I am running qiime2-2019.10 in a conda env with python 3.7.3 in a docker container.

thanks!

I have now gotten this working, I had made a mistake while installing fastspar. so i reinstalled it using the following command

conda install -c bioconda -c conda-forge fastspar

2 Likes

So I tried

conda install -c bioconda -c conda-forge fastspar

and get stuck in a solving environment loop. Anyone else have this problem?