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Description
command line:
mavisp -d /data/raw_data/computational_data/mavisp_data_saturation/ -o 11112025_ALL -e ARID3A,CDKN2A-ARF -f
traceback:
Traceback (most recent call last):
File "/usr/local/envs/mavisp/bin/mavisp", line 8, in <module>
sys.exit(main())
~~~~^^
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/mavisp/mavisp.py", line 145, in main
mfs = MAVISpFileSystem( data_dir=in_path,
exclude_proteins=excluded_proteins,
include_proteins=included_proteins,
modes=args.modes)
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/mavisp/core.py", line 64, in __init__
self.dataset_tables[mode_name] = self._gen_dataset_table(mode, include=include_proteins, exclude=exclude_proteins)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/mavisp/core.py", line 93, in _gen_dataset_table
metadata, metadata_mavisp_criticals = mode.parse_metadata(self.data_dir, system)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/mavisp/modes.py", line 98, in parse_metadata
metadata = self._parse_metadata_file(data_dir, system, self.name)
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/mavisp/modes.py", line 34, in _parse_metadata_file
return yaml.safe_load(fh)
~~~~~~~~~~~~~~^^^^
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/yaml/__init__.py", line 125, in safe_load
return load(stream, SafeLoader)
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/yaml/__init__.py", line 81, in load
return loader.get_single_data()
~~~~~~~~~~~~~~~~~~~~~~^^
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/yaml/constructor.py", line 49, in get_single_data
node = self.get_single_node()
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/yaml/composer.py", line 36, in get_single_node
document = self.compose_document()
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/yaml/composer.py", line 55, in compose_document
node = self.compose_node(None, None)
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/yaml/composer.py", line 84, in compose_node
node = self.compose_mapping_node(anchor)
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/yaml/composer.py", line 127, in compose_mapping_node
while not self.check_event(MappingEndEvent):
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/yaml/parser.py", line 98, in check_event
self.current_event = self.state()
~~~~~~~~~~^^
File "/usr/local/envs/mavisp/lib/python3.13/site-packages/yaml/parser.py", line 438, in parse_block_mapping_key
raise ParserError("while parsing a block mapping", self.marks[-1],
"expected <block end>, but found %r" % token.id, token.start_mark)
yaml.parser.ParserError: while parsing a block mapping
in "/data/raw_data/computational_data/mavisp_data_saturation/AMER1/simple_mode/metadata.yaml", line 1, column 1
expected <block end>, but found '-'
in "/data/raw_data/computational_data/mavisp_data_saturation/AMER1/simple_mode/metadata.yaml", line 8, column 1
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