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print nice error when can't find config file

Open bluegenes opened this issue 4 years ago • 0 comments

current output is not super user-friendly :)

charcoal run orthodb.conf -n

Traceback (most recent call last):
  File "/home/ntpierce/miniconda3/envs/charcoal/lib/python3.8/site-packages/snakemake/io.py", line 1372, in _load_configfile
    with open(configpath) as f:
FileNotFoundError: [Errno 2] No such file or directory: 'orthodb.conf'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ntpierce/miniconda3/envs/charcoal/bin/snakemake", line 8, in <module>
    sys.exit(main())
  File "/home/ntpierce/miniconda3/envs/charcoal/lib/python3.8/site-packages/snakemake/__init__.py", line 2252, in main
    success = snakemake(
  File "/home/ntpierce/miniconda3/envs/charcoal/lib/python3.8/site-packages/snakemake/__init__.py", line 454, in snakemake
    overwrite_config.update(load_configfile(f))
  File "/home/ntpierce/miniconda3/envs/charcoal/lib/python3.8/site-packages/snakemake/io.py", line 1402, in load_configfile
    config = _load_configfile(configpath)
  File "/home/ntpierce/miniconda3/envs/charcoal/lib/python3.8/site-packages/snakemake/io.py", line 1397, in _load_configfile
    raise WorkflowError("{} file {} not found.".format(filetype, configpath))
snakemake.exceptions.WorkflowError: Config file orthodb.conf not found.
Error in snakemake invocation: Command '['snakemake', '-s', '/home/ntpierce/charcoal/charcoal/Snakefile', '--use-conda', '-j', '1', '-n', '--configfile', '/home/ntpierce/charcoal/charcoal/conf/defaults.conf', '/home/ntpierce/charcoal/charcoal/conf/system.conf', 'orthodb.conf']' returned non-zero exit status 1.

bluegenes avatar Jun 05 '20 15:06 bluegenes