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Error using UniProt to create a table with protein accessions and GO annotations #4

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kalonji08 opened this issue Mar 22, 2023 · 0 comments

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@kalonji08
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Hi i have run the following code
./main.py prepare_uniprot_files -u /media/kalonjilab2/kalonjiPhD/DB_Pies/uniprot_sprot.dat.gz -t /media/kalonjilab2/kalonjiPhD/DB_Pies/sprot.table.gz

and i got this error

NCBI database not present yet (first time used?)
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...
Loading node names...
2495320 names loaded.
300644 synonyms loaded.
Loading nodes...
2495320 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /home/kalonjilab2/.etetoolkit/taxa.sqlite ...
2495000 generating entries...
Uploading to /home/kalonjilab2/.etetoolkit/taxa.sqlite

Inserting synonyms: 300000
Inserting taxid merges: 70000
Inserting taxids: 2495000
Traceback (most recent call last):
File "/home/kalonjilab2/miniconda3/envs/mpies/lib/python3.9/logging/config.py", line 564, in configure
handler = self.configure_handler(handlers[name])
File "/home/kalonjilab2/miniconda3/envs/mpies/lib/python3.9/logging/config.py", line 745, in configure_handler
result = factory(**kwargs)
File "/home/kalonjilab2/miniconda3/envs/mpies/lib/python3.9/logging/handlers.py", line 153, in init
BaseRotatingHandler.init(self, filename, mode, encoding=encoding,
File "/home/kalonjilab2/miniconda3/envs/mpies/lib/python3.9/logging/handlers.py", line 58, in init
logging.FileHandler.init(self, filename, mode=mode,
File "/home/kalonjilab2/miniconda3/envs/mpies/lib/python3.9/logging/init.py", line 1132, in init
filename = os.fspath(filename)
TypeError: expected str, bytes or os.PathLike object, not NoneType

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

Traceback (most recent call last):
File "/home/kalonjilab2/mPies/./main.py", line 279, in
main()
File "/home/kalonjilab2/mPies/./main.py", line 192, in main
logger = configure_logger(name="mptk_" + args.mode, log_file=args.log_file, level=lvl)
File "/home/kalonjilab2/mPies/./main.py", line 31, in configure_logger
logging.config.dictConfig({
File "/home/kalonjilab2/miniconda3/envs/mpies/lib/python3.9/logging/config.py", line 809, in dictConfig
dictConfigClass(config).configure()
File "/home/kalonjilab2/miniconda3/envs/mpies/lib/python3.9/logging/config.py", line 571, in configure
raise ValueError('Unable to configure handler '
ValueError: Unable to configure handler 'file'

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