ligo,uio-bmi

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LIgO is a tool for simulation of adaptive immune receptors and repertoires.

License: GNU Affero General Public License v3.0

Dockerfile 0.03% Python 97.23% HTML 2.25% CSS 0.32% Shell 0.01% Makefile 0.07% Batchfile 0.09%

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No repertoires generated in output

Hello there - thanks for making this very interesting tool! I have installed LigO in a virtual environment as suggested, running Python 3.11.0rc1. All dependencies were installed without errors. On running the provided quickstart example, I receive the following output:


> (ligo_env) aag7319@aag7319-MS-7C91:~$ ligo specs.yaml output_folder
> 2023-11-02 14:38:37.703487: LIgO: parsing the specification...
> 2023-11-02 14:38:39.077426: Full specification is available at output_folder/full_specs.yaml.
> 2023-11-02 14:38:39.077473: LIgO: starting the simulation...
> 2023-11-02 14:38:39.078744: Generating HTML reports...
> 2023-11-02 14:38:39.078796: HTML reports are generated.
> 2023-11-02 14:38:39.078818: LIgO: finished simulation.

On examination, my output folder only contains full_specs.yaml and log.txt. Log reports no errors and shows the following:

2023-11-02 14:43:51,727 INFO: LIgO: parsing the specification...

2023-11-02 14:43:51,743 INFO: --- Entering: _parse_seed_motif with parameters ('motif1', {'seed': 'AS'})
2023-11-02 14:43:51,743 INFO: --- Exiting: _parse_seed_motif
2023-11-02 14:43:51,743 INFO: --- Entering: _parse_seed_motif with parameters ('motif2', {'seed': 'G/G', 'max_gap': 2, 'min_gap': 1})
2023-11-02 14:43:51,743 INFO: --- Exiting: _parse_seed_motif
2023-11-02 14:43:51,743 INFO: --- Entering: parse with parameters ({'signal1': {'v_call': 'TRBV7', 'motifs': ['motif1']}, 'signal2': {'motifs': ['motif2']}}, SymbolTable())
2023-11-02 14:43:51,743 INFO: --- Exiting: parse
2023-11-02 14:43:53,084 INFO: Full specification is available at output_folder/full_specs.yaml.

2023-11-02 14:43:53,084 INFO: LIgO: starting the simulation...

2023-11-02 14:43:53,085 INFO: Generating HTML reports...
2023-11-02 14:43:53,086 INFO: HTML reports are generated.
2023-11-02 14:43:53,086 INFO: LIgO: finished simulation.

Any help would be appreciated - thanks!

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