Document when you can reduce and/or discard_per_amino_acid_embeddings about bio_embeddings HOT 2 CLOSED

 80%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▊                                   | 4/5 [00:03<00:00,  1.24it/s]
Traceback (most recent call last):
  File "/home/kschuetze/bio_embeddings/.venv/bin/bio_embeddings", line 33, in <module>
    sys.exit(load_entry_point('bio-embeddings', 'console_scripts', 'bio_embeddings')())
  File "/home/kschuetze/bio_embeddings/bio_embeddings/utilities/cli.py", line 24, in main
    parse_config_file_and_execute_run(arguments.config_path[0], overwrite=arguments.overwrite)
  File "/home/kschuetze/bio_embeddings/bio_embeddings/utilities/pipeline.py", line 202, in parse_config_file_and_execute_run
    execute_pipeline_from_config(config, **kwargs)
  File "/home/kschuetze/bio_embeddings/bio_embeddings/utilities/pipeline.py", line 169, in execute_pipeline_from_config
    stage_output_parameters = stage_runnable(**stage_parameters)
  File "/home/kschuetze/bio_embeddings/bio_embeddings/extract/pipeline.py", line 158, in run
    return PROTOCOLS[kwargs["protocol"]](**kwargs)
  File "/home/kschuetze/bio_embeddings/bio_embeddings/extract/pipeline.py", line 31, in seqvec_from_publication
    return predict_annotations_using_basic_models("seqvec_from_publication", **kwargs)
  File "/home/kschuetze/bio_embeddings/bio_embeddings/extract/pipeline.py", line 48, in predict_annotations_using_basic_models
    check_required(kwargs, ['embeddings_file', 'mapping_file', 'remapped_sequences_file'])
  File "/home/kschuetze/bio_embeddings/bio_embeddings/utilities/helpers.py", line 32, in check_required
    ", ".join(missing), params
bio_embeddings.utilities.exceptions.MissingParameterError: Missing required parameters: embeddings_file 
Given: {'sequences_file': 'simple/sequences_file.fasta', 'prefix': 'simple', 'simple_remapping': False, 'mapping_file': 'simple/mapping_file.csv', 'remapped_sequences_file': 'simple/remapped_sequences_file.fasta', 'type': 'extract', 'protocol': 'seqvec_from_publication', 'reduce': True, 'discard_per_amino_acid_embeddings': True, 'weights_file': '/mnt/nfs/models/seqvec/weights_file', 'options_file': '/mnt/nfs/models/seqvec/options_file', 'stage_name': 'annotations_from_seqvec', 'start_time': '2020-09-05 22:24:30.492982+02:00', 'max_amino_acids': 15000, 'reduced_embeddings_file': 'simple/seqvec_embeddings/reduced_embeddings_file.h5', 'end_time': '2020-09-05 22:24:30.490852+02:00', 'elapsed_time': '0:00:26.489258', 'depends_on': 'seqvec_embeddings'}