Python error

[holzdan]

Hi i just downloaded bakta 1.9.4 and the ver 5 light database . ive run the pipeline against an example . this is the error i get (base) xxx@xxx-X470-AORUS-ULTRA-GAMING:~/Downloads/bakta-1.9.4/bin$ /home/xxx/Downloads/bakta-1.9.4/bin/bakta --db /home/xxx/Downloads/bakta-1.9.4/bin/db5light sequence.fasta --output test5 --debug --skip-ncrna --skip-crisp
Bakta v1.9.4
Options and arguments:
input: /home/xxx/Downloads/bakta-1.9.4/bin/sequence.fasta
db: /home/xxx/Downloads/bakta-1.9.4/bin/db5light, version 5.1, light
output: /home/xxx/Downloads/bakta-1.9.4/bin/test5
tmp directory: /tmp/tmppi1a65fk
prefix: sequence
threads: 12
debug: True
translation table: 11
skip ncRNA: True
skip CRISPR: True

Bakta runs in DEBUG mode! Temporary data will not be destroyed at: /tmp/tmppi1a65fk

parse genome sequences...
imported: 1
filtered & revised: 1
contigs: 1

start annotation...
predict tRNAs...
found: 41
predict tmRNAs...
found: 1
predict rRNAs...
found: 11
skip ncRNA prediction...
predict ncRNA regions...
found: 7
skip CRISPR array prediction...
predict & annotate CDSs...
predicted: 4344
discarded spurious: 4
revised translational exceptions: 0
--- Logging error ---
Traceback (most recent call last):
File "/home/xxx/Downloads/bakta-1.9.4/bakta/ups.py", line 43, in lookup
if(rec is not None and rec[DB_UPS_COL_LENGTH] == len(feature['aa'])):
~~~^^^^^^^^^^^^^^^^^^^
IndexError: tuple index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/xxx/miniconda3/lib/python3.12/logging/init.py", line 1160, in emit
msg = self.format(record)
^^^^^^^^^^^^^^^^^^^
File "/home/xxx/miniconda3/lib/python3.12/logging/init.py", line 999, in format
return fmt.format(record)
^^^^^^^^^^^^^^^^^^
File "/home/xxx/miniconda3/lib/python3.12/logging/init.py", line 703, in format
record.message = record.getMessage()
^^^^^^^^^^^^^^^^^^^
File "/home/xxx/miniconda3/lib/python3.12/logging/init.py", line 392, in getMessage
msg = msg % self.args
~~~~^~~~~~~~~~~
TypeError: not all arguments converted during string formatting
Call stack:
File "", line 198, in _run_module_as_main
File "", line 88, in _run_code
File "/home/xxx/Downloads/bakta-1.9.4/bakta/main.py", line 619, in
main()
File "/home/xxx/Downloads/bakta-1.9.4/bakta/main.py", line 251, in main
cdss_ups, cdss_not_found = ups.lookup(cdss)
File "/home/xxx/Downloads/bakta-1.9.4/bakta/ups.py", line 57, in lookup
log.exception('Could not read UPSs from db!', ex)
Message: 'Could not read UPSs from db!'
Arguments: (IndexError('tuple index out of range'),)
Traceback (most recent call last):
File "/home/xxx/Downloads/bakta-1.9.4/bakta/ups.py", line 43, in lookup
if(rec is not None and rec[DB_UPS_COL_LENGTH] == len(feature['aa'])):
~~~^^^^^^^^^^^^^^^^^^^
IndexError: tuple index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "", line 198, in _run_module_as_main
File "", line 88, in _run_code
File "/home/xxx/Downloads/bakta-1.9.4/bakta/main.py", line 619, in
main()
File "/home/xxx/Downloads/bakta-1.9.4/bakta/main.py", line 251, in main
cdss_ups, cdss_not_found = ups.lookup(cdss)
^^^^^^^^^^^^^^^^
File "/home/xxx/Downloads/bakta-1.9.4/bakta/ups.py", line 58, in lookup
raise Exception("SQL error!", ex)
Exception: ('SQL error!', IndexError('tuple index out of range'))

heres the log

sequence.log

Do you have an idea how to fix this ?
i tried running the installation via conda but unfortunately i got the pyrodigal error : AttributeError: module 'pyrodigal' has no attribute 'OrfFinder' and so i tried to run the 1.9.4 version.