dcroote / singlecell-ige Goto Github PK

Hi @dcroote ,

I was trying to run the pipeline on my Mac, and ran into an error. I wondered if there is any clue about this error. Thanks!

% snakemake --use-conda --cores 4
Multiple include of /Users/kh/Softwares/singlecell-ige/rules/common.smk ignored
Building DAG of jobs...
Traceback (most recent call last):
File "/Users/kh/Softwares/mambaforge/envs/IgE_snakemake/lib/python3.5/site-packages/snakemake/init.py", line 647, in snakemake
keepincomplete=keep_incomplete,
File "/Users/kh/Softwares/mambaforge/envs/IgE_snakemake/lib/python3.5/site-packages/snakemake/workflow.py", line 777, in execute
quiet=list_conda_envs,
File "/Users/kh/Softwares/mambaforge/envs/IgE_snakemake/lib/python3.5/site-packages/snakemake/dag.py", line 260, in create_conda_envs
env.create(dryrun)
File "/Users/kh/Softwares/mambaforge/envs/IgE_snakemake/lib/python3.5/site-packages/snakemake/deployment/conda.py", line 232, in create
conda = Conda(self._container_img)
File "/Users/kh/Softwares/mambaforge/envs/IgE_snakemake/lib/python3.5/site-packages/snakemake/deployment/conda.py", line 343, in new
inst.init(container_img=container_img)
File "/Users/kh/Softwares/mambaforge/envs/IgE_snakemake/lib/python3.5/site-packages/snakemake/deployment/conda.py", line 357, in init
self.info = json.loads(shell.check_output(self._get_cmd("conda info --json")))
File "/Users/kh/Softwares/mambaforge/envs/IgE_snakemake/lib/python3.5/json/init.py", line 312, in loads
s.class.name))
TypeError: the JSON object must be str, not 'bytes'