Demande d'installation de "Dram" et "Dram-v" avec les banque de donnée pour Dram

IFB Core Cluster Demande de logiciel ou de banque de données
1

Bonjour/Bonsoir,

Serait-il possible d'installer les programmes "Dram/Dram-V" sur le cluster ? (sans ou avec KEGG, pas de différence)

Merci pour votre temps,

Emily

@team.ifbcorecluster

2

Installation en cours :

3

Hop:

module load dram/1.3.5
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4

Bonjour @gildaslecorguille @team.ifbcorecluster
Je pense qu'il y a un problème avec les banque de donnée pour Dram.
J'ai inclus l'erreur. Merci

/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/lib/python3.10/site-packages/mag_annotator/database_handler.py:51: UserWarning: Database does not exist at path None
  warnings.warn('Database does not exist at path %s' % self.description_loc)
/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/lib/python3.10/site-packages/mag_annotator/annotate_bins.py:802: UserWarning: No KEGG source provided so distillation will be of limited use.
  warnings.warn('No KEGG source provided so distillation will be of limited use.')
/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/lib/python3.10/site-packages/mag_annotator/annotate_bins.py:603: UserWarning: No rRNAs were detected, no rrnas.tsv file will be created.
  warnings.warn('No rRNAs were detected, no rrnas.tsv file will be created.')
Traceback (most recent call last):
  File "/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/bin/DRAM-v.py", line 153, in <module>
    args.func(**args_dict)
  File "/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/lib/python3.10/site-packages/mag_annotator/annotate_vgfs.py", line 481, in annotate_vgfs
    annotations = add_dramv_scores_and_flags(annotations, db_handler, virsorter_hits, input_fasta)
  File "/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/lib/python3.10/site-packages/mag_annotator/annotate_vgfs.py", line 383, in add_dramv_scores_and_flags
    amg_database_frame = pd.read_csv(db_handler.dram_sheet_locs['amg_database'], sep='\t')
  File "/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/lib/python3.10/site-packages/pandas/util/_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)
  File "/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 575, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 934, in __init__
    self._engine = self._make_engine(f, self.engine)
  File "/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1218, in _make_engine
    self.handles = get_handle(  # type: ignore[call-overload]
  File "/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/lib/python3.10/site-packages/pandas/io/common.py", line 667, in get_handle
    ioargs = _get_filepath_or_buffer(
  File "/shared/ifbstor1/software/miniconda/envs/dram-1.3.5/lib/python3.10/site-packages/pandas/io/common.py", line 424, in _get_filepath_or_buffer
    raise ValueError(msg)
ValueError: Invalid file path or buffer object type: <class 'NoneType'>
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Désolé, je n'ai pas pris le temps de gérer la banque :confused:

6

C'est en cours : /shared/bank/dram/2022-07

Le numéro de job est le 24477969 :crossed_fingers:
(sacct -j 24477969)

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7

Pas de problème ! Merci beaucoup et bonne jounée !

Emily