TypeError: the JSON object must be str, not 'bytes'

[huangk3]

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'

[dcroote]

Hi @huangk3 - I think it may have to do with the snakemake version. Can you provide the output of the following:

snakemake --version
conda --version

[huangk3]

Thanks for the response @dcroote. Here is the version info:

% snakemake --version
5.11.1
% conda --version
conda 4.10.3

[dcroote]

Thanks @huangk3, I was able to reproduce your error with snakemake 5.11.1. Can you please downgrade to snakemake 5.2.4? If you created the conda env via the instructions in the readme, you should be able to do this via conda remove -y snakemake-minimal && conda install -y snakemake-minimal=5.2.4.

[huangk3]

The error is gone after installed snakemake v5.2.4. Thanks for the help! @dcroote