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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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KeyError: 'amg_database' in DRAM-v #289

Open nologo68 opened 11 months ago

nologo68 commented 11 months ago

I was running DRAM-v to annotate some VirSorter2 results before distillation, but in the error file I got this:

/mnt/home/soft/dramv/programs/x86_64/1.4.6/lib/python3.9/site-packages/mag_annotator/database_handler.py:123: UserWarning: Database does not exist at path None warnings.warn("Database does not exist at path %s" % description_loc) /mnt/home/soft/dramv/programs/x86_64/1.4.6/lib/python3.9/site-packages/mag_annotator/database_handler.py:537: UserWarning: Sequences will not be annoated against VOGDB as it is not configured for use in DRAM warnings.warn( 2023-07-27 11:36:12,402 - 1 fastas found 2023-07-27 11:36:12,403 - Checking for duplicate names 2023-07-27 11:36:12,623 - No duplicate names found 2023-07-27 11:36:12,624 - Starting the Viral Annotation of Genes with database configuration:

2023-07-27 11:36:12,627 - Retrieved database locations and descriptions 2023-07-27 11:36:12,627 - Annotating final-viral-combined-for-dramv 2023-07-27 11:48:20,796 - Turning genes from prodigal to mmseqs2 db 2023-07-27 11:48:25,234 - No KEGG source provided so distillation will be of limited use. 2023-07-27 11:48:33,287 - Merging ORF annotations 2023-07-27 16:02:27,738 - Annotations complete, processing annotations Traceback (most recent call last): File "/mnt/home/soft/dramv/programs/x86_64/1.4.6/bin/DRAM-v.py", line 161, in args.func(**args_dict) File "/mnt/home/soft/dramv/programs/x86_64/1.4.6/lib/python3.9/site-packages/mag_annotator/annotate_vgfs.py", line 507, in annotate_vgfs annotations = add_dramv_scores_and_flags(annotations, db_handler, logger, virsorter_hits, input_fasta) File "/mnt/home/soft/dramv/programs/x86_64/1.4.6/lib/python3.9/site-packages/mag_annotator/annotate_vgfs.py", line 385, in add_dramv_scores_and_flags amg_database_frame = pd.read_csv(db_handler.config['dram_sheets']['amg_database'], sep='\t') KeyError: 'amg_database'

TJrogers86 commented 6 months ago

Did you ever figure out this issue?

alexandra-valeanu commented 1 month ago

@nologo68 , @TJrogers86 did you manage to solve this error?