SQL error

[chenolaf]

Loading requirement: Blast+/2.14.0 diamond/2.1.10 aragorn/1.2.41 pilercr/1.06
tRNAscan-SE/2.0.11 infernal/1.1.4 amrfinder/v4.0.3
--- Logging error ---
Traceback (most recent call last):
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/envs/bakta/lib/python3.10/site-packages/bakta/pscc.py", line 120, in lookup
rec = future.result()
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/lib/python3.10/concurrent/futures/_base.py", line 451, in result
return self.__get_result()
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
raise self._exception
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/lib/python3.10/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/envs/bakta/lib/python3.10/site-packages/bakta/pscc.py", line 145, in fetch_db_pscc_result
c.execute('select * from pscc where uniref50_id=?', (uniref50_id,))
sqlite3.DatabaseError: malformed database schema (pscc) - near "WITHOUT": syntax error

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/lib/python3.10/logging/init.py", line 1100, in emit
msg = self.format(record)
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/lib/python3.10/logging/init.py", line 943, in format
return fmt.format(record)
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/lib/python3.10/logging/init.py", line 678, in format
record.message = record.getMessage()
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/lib/python3.10/logging/init.py", line 368, in getMessage
msg = msg % self.args
TypeError: not all arguments converted during string formatting
Call stack:
File "/biostack/tools/devtools/pyenv/2.5.2/versions/bakta//bin/bakta", line 8, in
sys.exit(main())
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/envs/bakta/lib/python3.10/site-packages/bakta/main.py", line 294, in main
pscc.lookup(cdss) # lookup PSCC info
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/envs/bakta/lib/python3.10/site-packages/bakta/pscc.py", line 138, in lookup
log.exception('Could not read PSCCs from db!', ex)
Message: 'Could not read PSCCs from db!'
Arguments: (DatabaseError('malformed database schema (pscc) - near "WITHOUT": syntax error'),)
Parse genome sequences...
imported: 164
filtered & revised: 164
contigs: 164

Start annotation...
predict tRNAs...
found: 50
predict tmRNAs...
found: 1
predict rRNAs...
found: 3
predict ncRNAs...
found: 15
predict ncRNA regions...
found: 23
predict CRISPR arrays...
found: 0
predict & annotate CDSs...
predicted: 4824
discarded length: 0
discarded spurious: 4
revised translational exceptions: 1
skip UPS/IPS detection with light db version
found PSCCs: 3935
lookup annotations...
Traceback (most recent call last):
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/envs/bakta/lib/python3.10/site-packages/bakta/pscc.py", line 120, in lookup
rec = future.result()
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/lib/python3.10/concurrent/futures/_base.py", line 451, in result
return self.__get_result()
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
raise self._exception
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/lib/python3.10/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/envs/bakta/lib/python3.10/site-packages/bakta/pscc.py", line 145, in fetch_db_pscc_result
c.execute('select * from pscc where uniref50_id=?', (uniref50_id,))
sqlite3.DatabaseError: malformed database schema (pscc) - near "WITHOUT": syntax error

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/biostack/tools/devtools/pyenv/2.5.2/versions/bakta//bin/bakta", line 8, in
sys.exit(main())
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/envs/bakta/lib/python3.10/site-packages/bakta/main.py", line 294, in main
pscc.lookup(cdss) # lookup PSCC info
File "/biostack/tools/devtools/pyenv/2.5.2/versions/3.10.16/envs/bakta/lib/python3.10/site-packages/bakta/pscc.py", line 139, in lookup
raise Exception('SQL error!', ex)
Exception: ('SQL error!', DatabaseError('malformed database schema (pscc) - near "WITHOUT": syntax error'))