bgcflow run -n command

[coderbins]

(bgcflow) [n@login01 bgcflow]$ bgcflow init -n
Usage: bgcflow init [OPTIONS]
Try 'bgcflow init -h' for help.

Error: No such option: -n
(bgcflow) [n@login01 bgcflow]$ bgcflow init
DEBUG	23/09 12:30:14   Found config file at: /home/n/bgcflow/bgcflow/config/config.yaml
DEBUG	23/09 12:30:14   Creating Project from file /home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/project_config.yaml
DEBUG	23/09 12:30:14   Creating a Project from a YAML file: /home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/project_config.yaml
DEBUG	23/09 12:30:14   Raw (/home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/project_config.yaml) config data: {'name': 'Lactobacillus_delbrueckii', 'pep_version': '2.1.0', 'description': 'Lactobacillus delbrueckii 27 01 2023', 'sample_table': 'samples.csv', 'rules': {'seqfu': True, 'mash': True, 'fastani': True, 'checkm': True, 'gtdbtk': False, 'prokka-gbk': True, 'antismash': True, 'query-bigslice': False, 'bigscape': True, 'bigslice': True, 'automlst-wrapper': True, 'arts': True, 'roary': False, 'eggnog': False, 'eggnog-roary': False, 'deeptfactor': True, 'deeptfactor-roary': False, 'cblaster-genome': True, 'cblaster-bgc': False, 'gecco': True, 'amrfinderplus': False}}
DEBUG	23/09 12:30:14   Adding attributes: name, pep_version, description, sample_table, rules
DEBUG	23/09 12:30:14   Ensuring absolute path for 'samples.csv'
DEBUG	23/09 12:30:14   config_dirpath: /home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii
DEBUG	23/09 12:30:14   Expanded and/or made absolute: /home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/samples.csv
DEBUG	23/09 12:30:14   Setting 'sample_table' to '/home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/samples.csv'
DEBUG	23/09 12:30:14   No 'subsample_table' section in configuration file: /home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/project_config.yaml
DEBUG	23/09 12:30:14   No subsample_table specified
DEBUG	23/09 12:30:14   Sample data: OrderedDict([('genome_id', 'GCA_000056065.1'), ('source', 'ncbi'), ('organism', None), ('genus', None), ('species', None), ('strain', None), ('closest_placement_reference', None), ('input_file', None)])
DEBUG	23/09 12:30:14   Sample data: OrderedDict([('genome_id', 'GCA_000182835.1'), ('source', 'ncbi'), ('organism', None), ('genus', None), ('species', None), ('strain', None), ('closest_placement_reference', None), ('input_file', None)])
DEBUG	23/09 12:30:14   Sample data: OrderedDict([('genome_id', 'GCA_000191165.1'), ('source', 'ncbi'), ('organism', None), ('genus', None), ('species', None), ('strain', None), ('closest_placement_reference', None), ('input_file', None)])
DEBUG	23/09 12:30:14   Sample data: OrderedDict([('genome_id', 'GCA_000014405.1'), ('source', 'ncbi'), ('organism', None), ('genus', None), ('species', None), ('strain', None), ('closest_placement_reference', None), ('input_file', None)])
DEBUG	23/09 12:30:14   Checking existence: None
DEBUG	23/09 12:30:14   Checking existence: remove
DEBUG	23/09 12:30:14   Checking existence: append
DEBUG	23/09 12:30:14   Checking existence: duplicate
DEBUG	23/09 12:30:14   Checking existence: imply
DEBUG	23/09 12:30:14   No subsample_table found, skipping merge
DEBUG	23/09 12:30:14   Checking existence: derive
DEBUG	23/09 12:30:14   Checking existence: None
DEBUG	23/09 12:30:14   Setting sample_table index to: ['genome_id']
Available projects:
 - Lactobacillus_delbrueckii : /home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/samples.csv

Do a test run by: `bgcflow run -n`

(bgcflow) [n@login01 bgcflow]$ bgcflow run -n
Monitoring BGCFlow jobs with Panoptes...
DEBUG	23/09 12:30:32   Starting new HTTP connection (1): 127.0.0.1:5000
DEBUG	23/09 12:30:32   http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 200 21
Panoptes already running on http://127.0.0.1:5000
Connecting to Panoptes...
DEBUG	23/09 12:30:32   Starting new HTTP connection (1): 127.0.0.1:5000
DEBUG	23/09 12:30:32   http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 200 21
Panoptes status: running

DEBUG: Using 8 out of 80 available cores

Running Snakemake with command:
cd . && snakemake --snakefile workflow/Snakefile --use-conda --keep-going --rerun-incomplete --rerun-triggers mtime -c 8 --dryrun 	--wms-monitor http://127.0.0.1:5000
Traceback (most recent call last):

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/requests/models.py", line 974, in json
	return complexjson.loads(self.text, **kwargs)
       	^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/json/__init__.py", line 346, in loads
	return _default_decoder.decode(s)
       	^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/json/decoder.py", line 337, in decode
	obj, end = self.raw_decode(s, idx=_w(s, 0).end())
           	^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/json/decoder.py", line 355, in raw_decode
	raise JSONDecodeError("Expecting value", s, err.value) from None

json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)


During handling of the above exception, another exception occurred:


Traceback (most recent call last):

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py", line 2155, in main
	success = args_to_api(args, parser)
          	^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py", line 1896, in args_to_api
	log_handlers = setup_log_handlers(args, parser)
               	^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py", line 1807, in setup_log_handlers
	wms_logger = logging.WMSLogger(
             	^^^^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/snakemake/logging.py", line 148, in __init__
	self.create_workflow()

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/snakemake/logging.py", line 199, in create_workflow
	id = response.json()["id"]
     	^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/requests/models.py", line 978, in json
	raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)

requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)