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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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ERROR: ('Error, plasmidfinder database type [{}] is either incorrect or plasmidfinder database not installed properly', 'enterobacteriaceae') #177

Closed qianxin-kxy closed 1 year ago

qianxin-kxy commented 1 year ago

Hello, very meaningful software! I would like to determine the plasmid status in the genome of hundreds of Acinetobacter baumannii strains under the infile folder. The code is as follows, and the corresponding error reports are also as follows. Is there a good solution? Or is it said that the software cannot analyze the plasmid situation of Acinetobacter baumannii?

(staramr) [kxy@zju infile]$ staramr search --plasmidfinder-database-type enterobacteriaceae -o out *.fasta

2023-06-02 21:44:39,948 WARNING: Using non-default ResFinder/PointFinder. This may lead to differences in the detected AMR genes depending on how the database files are structured.
2023-06-02 21:44:39,948 INFO: No --pointfinder-organism specified. Will not search the PointFinder databases
2023-06-02 21:44:39,948 ERROR: ('Error, plasmidfinder database type [{}] is either incorrect or plasmidfinder database not installed properly', 'enterobacteriaceae') Traceback (most recent call last): File "/data/users/kxy/miniconda3/envs/staramr/bin/staramr", line 68, in args.run_command(args) File "/data/users/kxy/miniconda3/envs/staramr/lib/python3.7/site-packages/staramr/subcommand/Search.py", line 337, in run 'database_type': args.plasmidfinder_database_type}) File "/data/users/kxy/miniconda3/envs/staramr/lib/python3.7/site-packages/staramr/databases/BlastDatabaseRepositories.py", line 161, in build_blast_database return PlasmidfinderBlastDatabase(self.get_repo_dir(database_name), options['database_type']) File "/data/users/kxy/miniconda3/envs/staramr/lib/python3.7/site-packages/staramr/blast/plasmidfinder/PlasmidfinderBlastDatabase.py", line 34, in init database_type) Exception: ('Error, plasmidfinder database type [{}] is either incorrect or plasmidfinder database not installed properly', 'enterobacteriaceae')

apetkau commented 1 year ago

As mentioned in https://github.com/phac-nml/staramr/issues/169, enterobacteriaceae is out of date and it should be enterobacteriales. Though why it didn't automatically switch I'm not sure.

Note if you leave --plasmidfinder-database-type as the default it will search using all the fasta files from the PlasmidFinder database.

qianxin-kxy commented 1 year ago

As mentioned in #169, enterobacteriaceae is out of date and it should be enterobacteriales. Though why it didn't automatically switch I'm not sure.

Note if you leave --plasmidfinder-database-type as the default it will search using all the fasta files from the PlasmidFinder database.

Thank you for your reply. After I update Staramr to the latest version of 0.9.1 and replace the code with $ staramr search --plasmidfinder-database-type enterobacteriales -o out *.fasta, it can run normally