Hi,
I am running the scifi exe file on cluster as a job, and am passing the configuration file at runtime using -c. It is throwing the following error.
scifi_L004
Traceback (most recent call last):
File "/.../anaconda3/envs/my_pymc_env/bin/scifi", line 11, in
load_entry_point('scifi', 'console_scripts', 'scifi')()
File "/.../anaconda3/envs/my_pymc_env/lib/python3.7/site-packages/pkg_resources/init.py", line 487, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/.../anaconda3/envs/my_pymc_env/lib/python3.7/site-packages/pkg_resources/init.py", line 2728, in load_entry_point
return ep.load()
File "/.../anaconda3/envs/my_pymc_env/lib/python3.7/site-packages/pkg_resources/init.py", line 2346, in load
return self.resolve()
File "/.../anaconda3/envs/my_pymc_env/lib/python3.7/site-packages/pkg_resources/init.py", line 2352, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/.../scifiRNA-seq/build/lib/scifi/init.py", line 171, in
sys.exit(main())
File "/.../scifiRNA-seq/build/lib/scifi/pipeline.py", line 152, in main
map_command(args, sample_name, sample_out_dir, r1_annotation, _CONFIG)
File "/.../scifiRNA-seq/build/lib/scifi/map.py", line 85, in map_command
submit_job(job, params)
File "/.../scifiRNA-seq/build/lib/scifi/job_control.py", line 41, in submit_job
array="" if array is not None else "", **params
KeyError: 'job_name'
afrendeiro
commented
3 years ago
Hi, I am running the scifi exe file on cluster as a job, and am passing the configuration file at runtime using -c. It is throwing the following error.
scifi:pipeline:L112 (main) [INFO] > scifi-RNA-seq pipeline scifi:pipeline:L137 (main) [INFO] > Samples to submit:
Please let me know what the issue is.
Thanks! Som