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Issue running CONJScan with Singularity #4

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AvogadroTheMole opened this issue Jul 13, 2021 · 0 comments
Open

Issue running CONJScan with Singularity #4

AvogadroTheMole opened this issue Jul 13, 2021 · 0 comments

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@AvogadroTheMole
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I have been trying to get CONJScan up and running for searching a large number of genomes. I have been having issues with the container recognising my file locations. I moved into the container (singularity shell) and have tried to run the commands. Two representative outputs are below. Common errors include saying the xml is not versioned, and complaining that some combo definitions/, definitions/profiles, profiles/definitions/ are missing.

Any help in getting this software up and running would be greatly appreciated.

Singularity> macsyfinder --models Conjugation typeT --models-dir Models/ --sequence-db test.faa --db-type ordered_replicon --profile-suffix .hmm
command used: /usr/local/bin/macsyfinder --models Conjugation typeT --models-dir Models/ --sequence-db test.faa --db-type ordered_replicon --profile-suffix .hmm

######################### Searching systems ##########################
Models Parsing
unable to parse model definition 'Conjugation/typeT' : The model definition typeT.xml is not versioned. Please update your model.
Traceback (most recent call last):
File "/usr/local/bin/macsyfinder", line 8, in
sys.exit(main())
File "/usr/local/lib/python3.8/dist-packages/macsypy/scripts/macsyfinder.py", line 874, in main
all_systems, rejected_clusters = search_systems(config, models, genes, profile_factory, logger)
File "/usr/local/lib/python3.8/dist-packages/macsypy/scripts/macsyfinder.py", line 491, in search_systems
parser.parse(models_def_to_detect)
File "/usr/local/lib/python3.8/dist-packages/macsypy/definition_parser.py", line 77, in parse
model_node = self._get_model_node(def_loc)
File "/usr/local/lib/python3.8/dist-packages/macsypy/definition_parser.py", line 102, in _get_model_node
raise MacsypyError(msg) from None
macsypy.error.MacsypyError: unable to parse model definition 'Conjugation/typeT' : The model definition typeT.xml is not versioned. Please update your model.

Singularity> macsyfinder --models typeT --models-dir Models/Conjugation --sequence-db test.faa --db-type ordered_replicon --profile-suffix .hmm
command used: /usr/local/bin/macsyfinder --models typeT --models-dir Models/Conjugation --sequence-db test.faa --db-type ordered_replicon --profile-suffix .hmm

######################### Searching systems ##########################
Traceback (most recent call last):
File "/usr/local/bin/macsyfinder", line 8, in
sys.exit(main())
File "/usr/local/lib/python3.8/dist-packages/macsypy/scripts/macsyfinder.py", line 874, in main
all_systems, rejected_clusters = search_systems(config, models, genes, profile_factory, logger)
File "/usr/local/lib/python3.8/dist-packages/macsypy/scripts/macsyfinder.py", line 473, in search_systems
models_loc_available = scan_models_dir(model_dir,
File "/usr/local/lib/python3.8/dist-packages/macsypy/registries.py", line 74, in scan_models_dir
new_model = ModelLocation(path=model_path,
File "/usr/local/lib/python3.8/dist-packages/macsypy/registries.py", line 181, in init
for definition in os.listdir(def_dir):
FileNotFoundError: [Errno 2] No such file or directory: 'Models/Conjugation/definitions/definitions'

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