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