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EI-CoreBioinformatics / minos

The labyrinth king judges your gene models.
GNU Lesser General Public License v3.0
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gmc 1.0 fails when --hpc_config is not supplied #22

Closed cschu closed 4 years ago

cschu commented 4 years ago 
Traceback (most recent call last):
  File "/tgac/software/testing/python_miniconda/4.5.4_py3.6_cs/x86_64/lib/python3.6/site-packages/snakemake/io.py", line 1352, in _load_configfile
    with open(configpath) as f:
FileNotFoundError: [Errno 2] No such file or directory: ''

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/ei/software/cb/gmc/1.0/x86_64/bin/gmc", line 11, in <module>
    sys.exit(main())
  File "/ei/software/cb/gmc/1.0/x86_64/lib/python3.6/site-packages/gmc/__main__.py", line 117, in main
    run_snakemake(snake, args.outdir, run_configuration_file, exe_env, dryrun=args.dryrun)
  File "/ei/software/cb/gmc/1.0/x86_64/lib/python3.6/site-packages/eicore/snakemake_helper.py", line 223, in run_snakemake
    use_singularity=True
  File "/tgac/software/testing/python_miniconda/4.5.4_py3.6_cs/x86_64/lib/python3.6/site-packages/snakemake/__init__.py", line 347, in snakemake
    configs = [load_configfile(f) for f in cluster_config]
  File "/tgac/software/testing/python_miniconda/4.5.4_py3.6_cs/x86_64/lib/python3.6/site-packages/snakemake/__init__.py", line 347, in <listcomp>
    configs = [load_configfile(f) for f in cluster_config]
  File "/tgac/software/testing/python_miniconda/4.5.4_py3.6_cs/x86_64/lib/python3.6/site-packages/snakemake/io.py", line 1382, in load_configfile
    config = _load_configfile(configpath)
  File "/tgac/software/testing/python_miniconda/4.5.4_py3.6_cs/x86_64/lib/python3.6/site-packages/snakemake/io.py", line 1377, in _load_configfile
    raise WorkflowError("{} file {} not found.".format(filetype, configpath))
snakemake.exceptions.WorkflowError: Config file  not found.