dbCAN ERROR

[francesco-ricci]

Hello,

keep having this ERROR:

2023-09-24 17:15:28,613 - Logging to console 2023-09-24 17:15:31,034 - The log file is created at /home/fricci/rp24/fra/analyses/ostreobium_bacteria_interactions/DRAM/annotation$ 2023-09-24 17:15:31,036 - 150 FASTAs found 2023-09-24 17:15:31,044 - Starting the Annotation of Bins with database configuration: there are no settings, the config is corrupted or too old. 2023-09-24 17:15:31,045 - Retrieved database locations and descriptions 2023-09-24 17:15:31,045 - Annotating 644_MAG.64 2023-09-24 17:16:39,894 - Turning genes from prodigal to mmseqs2 db 2023-09-24 17:16:42,108 - Getting forward best hits from kegg 2023-09-24 17:18:47,223 - Getting reverse best hits from kegg 2023-09-24 17:19:53,296 - Getting descriptions of hits from kegg 2023-09-24 17:22:54,143 - Getting forward best hits from peptidase 2023-09-24 17:23:04,281 - Getting reverse best hits from peptidase 2023-09-24 17:23:15,062 - Getting descriptions of hits from peptidase 2023-09-24 17:23:28,109 - Getting hits from pfam 2023-09-24 17:24:14,119 - Getting hits from dbCAN Traceback (most recent call last): File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1965, in _exec_single_co$ self.dialect.do_execute( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 921, in do_execute cursor.execute(statement, parameters) sqlite3.OperationalError: no such column: dbcan_description.ec

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/fricci/miniconda3_p3.9/envs/DRAM/bin/DRAM.py", line 207, in args.func(args_dict) File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1513, in annotate_b$ all_annotations = annotate_fastas( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1394, in annotate_f$ annotate_fasta( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1239, in annotate_f$ annotations = annotate_orfs( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1107, in annotate_o$ run_hmmscan( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/mag_annotator/utils.py", line 210, in run_hmmscan return formater(hits) File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 320, in dbcan_hmmsc$ hits_df[f"{db_name}_hits"] = hits_df[f"{db_name}_ids"].apply(description_pull) File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/pandas/core/series.py", line 4758, in apply return SeriesApply( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/pandas/core/apply.py", line 1201, in apply return self.apply_standard() File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/pandas/core/apply.py", line 1281, in apply_standard mapped = obj._map_values( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/pandas/core/base.py", line 921, in _map_values return algorithms.map_array(arr, mapper, na_action=na_action, convert=convert) File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/pandas/core/algorithms.py", line 1812, in map_array return lib.map_infer(values, mapper, convert=convert) File "lib.pyx", line 2917, in pandas._libs.lib.map_infer File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 313, in description_pull description_list = db_handler.get_descriptions( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/mag_annotator/database_handler.py", line 205, in get_descriptions descriptions = [ File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/mag_annotator/database_handler.py", line 208, in for des in self.session.query(description_class) File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/orm/query.py", line 2688, in all return self._iter().all() # type: ignore File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/orm/query.py", line 2842, in _iter result: Union[ScalarResult[_T], Result[_T]] = self.session.execute( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/orm/session.py", line 2262, in execute return self._execute_internal( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/orm/session.py", line 2144, in _execute_internal result: Result[Any] = compile_state_cls.orm_execute_statement( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/orm/context.py", line 293, in orm_execute_statement result = conn.execute( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1412, in execute return meth( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/sql/elements.py", line 515, in _execute_on_connection return connection._execute_clauseelement( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1635, in _execute_clauseelement ret = self._execute_context( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1844, in _execute_context return self._exec_single_context( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1984, in _exec_single_context self._handle_dbapi_exception( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2339, in _handle_dbapi_exception raise sqlalchemy_exception.with_traceback(exc_info[2]) from e File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1965, in _exec_single_context self.dialect.do_execute( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 921, in do_execute cursor.execute(statement, parameters) sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such column: dbcan_description.ec [SQL: SELECT dbcan_description.id AS dbcan_description_id, dbcan_description.description AS dbcan_description_description, dbcan_description.ec AS dbcan_description_ec FROM dbcan_description WHERE dbcan_description.id IN (?)] [parameters: ('AA2',)] (Background on this error at: https://sqlalche.me/e/20/e3q8) 2023-09-24 17:24:44,422 - The log file is created at /home/fricci/rp24/fra/analyses/ostreobium_bacteria_interactions/DRAM/genome_summaries/distill.log Traceback (most recent call last): File "/home/fricci/miniconda3_p3.9/envs/DRAM/bin/DRAM.py", line 207, in args.func(args_dict) File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/mag_annotator/summarize_genomes.py", line 631, in summarize_genomes annotations = pd.read_csv(input_file, sep='\t', index_col=0) File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 948, in read_csv return _read(filepath_or_buffer, kwds) File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 611, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1448, in init self._engine = self._make_engine(f, self.engine) File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1705, in _make_engine self.handles = get_handle( File "/home/fricci/miniconda3_p3.9/envs/DRAM/lib/python3.9/site-packages/pandas/io/common.py", line 863, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: '/home/fricci/rp24/fra/analyses/ostreobium_bacteria_interactions/DRAM/annotation/annotations.tsv'

Any idea how to fix it?

Thanks Fra