I download the docker image and tried to run germline pipeline of DIVIS following the guideline in README.
First, I tried the substeps in DIVIS. I tried to call variants by gatk after align step is done:
divis substep -s gatk4_haplotypecaller_germline -c config -o result/
However, there are error messages:
Traceback (most recent call last):
File "/usr/local/bin/divis", line 9, in <module>
load_entry_point('DIVIS==0.1', 'console_scripts', 'divis')()
File "/usr/local/lib/python3.5/dist-packages/DIVIS-0.1-py3.5.egg/divis/cli.py", line 41, in main
cli()
File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 700, in __call__
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 680, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 1027, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 873, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 508, in invoke
return callback(*args, **kwargs)
File "/usr/local/lib/python3.5/dist-packages/DIVIS-0.1-py3.5.egg/divis/cli.py", line 22, in substep
sub_step_run(step, preview, config_file, out_dir)
File "/usr/local/lib/python3.5/dist-packages/DIVIS-0.1-py3.5.egg/divis/substep.py", line 17, in sub_step_run
default_macros_file = DEFAULT_SUBSTEP_MACROS_DICT[step_name]
KeyError: 'gatk4_haplotypecaller_germline'
I download the docker image and tried to run germline pipeline of DIVIS following the guideline in README.
First, I tried the substeps in DIVIS. I tried to call variants by gatk after align step is done:
divis substep -s gatk4_haplotypecaller_germline -c config -o result/However, there are error messages:
Then I tried running the whole pipeline:
divis pipeline -f wes_germline -p -c config -o result/Still got error message:
can't find pipeline: wes_germlineWhat should I do?