I have downloaded database files but I do not know how to provide database location to the database_handler.py script. When I run the analysis I get the following error:
2023-05-18 13:08:45,507 - The log file is created at /home/saraswati/DRAM_TRIAL_ANNOTATION/ANNOTATION/annotate.log.
2023-05-18 13:08:45,507 - 9 FASTAs found
/home/saraswati/conda/anaconda3/envs/DRAM/lib/python3.10/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)
2023-05-18 13:08:45,509 - Starting the Annotation of Bins with database configuration:
2023-05-18 13:08:45,512 - Retrieved database locations and descriptions
2023-05-18 13:08:45,512 - Annotating A5_bin.15
2023-05-18 13:08:58,256 - Turning genes from prodigal to mmseqs2 db
2023-05-18 13:09:08,492 - No KEGG source provided so distillation will be of limited use.
2023-05-18 13:09:08,554 - Merging ORF annotations
2023-05-18 13:09:28,902 - No rRNAs were detected, no rrnas.tsv file will be created.
2023-05-18 13:09:31,828 - Annotating A6_bin.24
2023-05-18 13:10:01,600 - Turning genes from prodigal to mmseqs2 db
2023-05-18 13:10:11,534 - No KEGG source provided so distillation will be of limited use.
2023-05-18 13:10:11,625 - Merging ORF annotations
2023-05-18 13:10:35,889 - Annotating A1_bin.1
2023-05-18 13:10:42,710 - Turning genes from prodigal to mmseqs2 db
2023-05-18 13:10:52,621 - No KEGG source provided so distillation will be of limited use.
2023-05-18 13:10:52,689 - Merging ORF annotations
2023-05-18 13:11:26,552 - Annotating A3_bin.25
2023-05-18 13:11:41,206 - Turning genes from prodigal to mmseqs2 db
2023-05-18 13:11:51,278 - No KEGG source provided so distillation will be of limited use.
2023-05-18 13:11:51,362 - Merging ORF annotations
2023-05-18 13:12:18,012 - No rRNAs were detected, no rrnas.tsv file will be created.
2023-05-18 13:12:23,504 - Annotating A2_bin.18
2023-05-18 13:12:39,533 - Turning genes from prodigal to mmseqs2 db
2023-05-18 13:12:49,422 - No KEGG source provided so distillation will be of limited use.
2023-05-18 13:12:49,498 - Merging ORF annotations
2023-05-18 13:13:16,324 - Annotating A7_bin.1
2023-05-18 13:13:25,999 - Turning genes from prodigal to mmseqs2 db
2023-05-18 13:13:35,859 - No KEGG source provided so distillation will be of limited use.
2023-05-18 13:13:35,918 - Merging ORF annotations
2023-05-18 13:14:00,596 - Annotating A4_bin.15
2023-05-18 13:14:16,771 - Turning genes from prodigal to mmseqs2 db
2023-05-18 13:14:26,670 - No KEGG source provided so distillation will be of limited use.
2023-05-18 13:14:26,738 - Merging ORF annotations
2023-05-18 13:14:41,269 - Annotating A7_bin.19
2023-05-18 13:15:05,006 - Turning genes from prodigal to mmseqs2 db
2023-05-18 13:15:14,950 - No KEGG source provided so distillation will be of limited use.
2023-05-18 13:15:15,035 - Merging ORF annotations
2023-05-18 13:15:40,514 - No rRNAs were detected, no rrnas.tsv file will be created.
2023-05-18 13:15:44,730 - Annotating A3_bin.6
2023-05-18 13:16:01,109 - Turning genes from prodigal to mmseqs2 db
2023-05-18 13:16:11,011 - No KEGG source provided so distillation will be of limited use.
2023-05-18 13:16:11,085 - Merging ORF annotations
2023-05-18 13:16:36,771 - Annotations complete, processing annotations
2023-05-18 13:16:38,288 - Completed annotations
And when I run this command : DRAM-setup.py print_config, I get the following output:
(DRAM) [saraswati@hn1 DRAM_data]$ DRAM-setup.py print_config
2023-05-18 17:41:04,346 - Logging to console
/home/saraswati/conda/anaconda3/envs/DRAM/lib/python3.10/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)
Processed search databases
KEGG db: None
KOfam db: None
KOfam KO list: None
UniRef db: None
Pfam db: None
dbCAN db: None
RefSeq Viral db: None
MEROPS peptidase db: None
VOGDB db: None
Descriptions of search database entries
Pfam hmm dat: None
dbCAN family activities: None
VOG annotations: None
Description db: None
DRAM distillation sheets
Genome summary form: None
Module step form: None
ETC module database: None
Function heatmap form: None
AMG database: None
(DRAM) [saraswati@hn1 DRAM_data]$ conda activate DRAM
Can you help me resolve this so that I can run DRAM to analyze my MAGs?
Hi! @rmFlynn
I have downloaded database files but I do not know how to provide database location to the database_handler.py script. When I run the analysis I get the following error:
2023-05-18 13:08:45,507 - The log file is created at /home/saraswati/DRAM_TRIAL_ANNOTATION/ANNOTATION/annotate.log. 2023-05-18 13:08:45,507 - 9 FASTAs found /home/saraswati/conda/anaconda3/envs/DRAM/lib/python3.10/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) 2023-05-18 13:08:45,509 - Starting the Annotation of Bins with database configuration:
2023-05-18 13:08:45,512 - Retrieved database locations and descriptions 2023-05-18 13:08:45,512 - Annotating A5_bin.15 2023-05-18 13:08:58,256 - Turning genes from prodigal to mmseqs2 db 2023-05-18 13:09:08,492 - No KEGG source provided so distillation will be of limited use. 2023-05-18 13:09:08,554 - Merging ORF annotations 2023-05-18 13:09:28,902 - No rRNAs were detected, no rrnas.tsv file will be created. 2023-05-18 13:09:31,828 - Annotating A6_bin.24 2023-05-18 13:10:01,600 - Turning genes from prodigal to mmseqs2 db 2023-05-18 13:10:11,534 - No KEGG source provided so distillation will be of limited use. 2023-05-18 13:10:11,625 - Merging ORF annotations 2023-05-18 13:10:35,889 - Annotating A1_bin.1 2023-05-18 13:10:42,710 - Turning genes from prodigal to mmseqs2 db 2023-05-18 13:10:52,621 - No KEGG source provided so distillation will be of limited use. 2023-05-18 13:10:52,689 - Merging ORF annotations 2023-05-18 13:11:26,552 - Annotating A3_bin.25 2023-05-18 13:11:41,206 - Turning genes from prodigal to mmseqs2 db 2023-05-18 13:11:51,278 - No KEGG source provided so distillation will be of limited use. 2023-05-18 13:11:51,362 - Merging ORF annotations 2023-05-18 13:12:18,012 - No rRNAs were detected, no rrnas.tsv file will be created. 2023-05-18 13:12:23,504 - Annotating A2_bin.18 2023-05-18 13:12:39,533 - Turning genes from prodigal to mmseqs2 db 2023-05-18 13:12:49,422 - No KEGG source provided so distillation will be of limited use. 2023-05-18 13:12:49,498 - Merging ORF annotations 2023-05-18 13:13:16,324 - Annotating A7_bin.1 2023-05-18 13:13:25,999 - Turning genes from prodigal to mmseqs2 db 2023-05-18 13:13:35,859 - No KEGG source provided so distillation will be of limited use. 2023-05-18 13:13:35,918 - Merging ORF annotations 2023-05-18 13:14:00,596 - Annotating A4_bin.15 2023-05-18 13:14:16,771 - Turning genes from prodigal to mmseqs2 db 2023-05-18 13:14:26,670 - No KEGG source provided so distillation will be of limited use. 2023-05-18 13:14:26,738 - Merging ORF annotations 2023-05-18 13:14:41,269 - Annotating A7_bin.19 2023-05-18 13:15:05,006 - Turning genes from prodigal to mmseqs2 db 2023-05-18 13:15:14,950 - No KEGG source provided so distillation will be of limited use. 2023-05-18 13:15:15,035 - Merging ORF annotations 2023-05-18 13:15:40,514 - No rRNAs were detected, no rrnas.tsv file will be created. 2023-05-18 13:15:44,730 - Annotating A3_bin.6 2023-05-18 13:16:01,109 - Turning genes from prodigal to mmseqs2 db 2023-05-18 13:16:11,011 - No KEGG source provided so distillation will be of limited use. 2023-05-18 13:16:11,085 - Merging ORF annotations 2023-05-18 13:16:36,771 - Annotations complete, processing annotations 2023-05-18 13:16:38,288 - Completed annotations
And when I run this command : DRAM-setup.py print_config, I get the following output: (DRAM) [saraswati@hn1 DRAM_data]$ DRAM-setup.py print_config 2023-05-18 17:41:04,346 - Logging to console /home/saraswati/conda/anaconda3/envs/DRAM/lib/python3.10/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) Processed search databases KEGG db: None KOfam db: None KOfam KO list: None UniRef db: None Pfam db: None dbCAN db: None RefSeq Viral db: None MEROPS peptidase db: None VOGDB db: None
Descriptions of search database entries Pfam hmm dat: None dbCAN family activities: None VOG annotations: None
Description db: None
DRAM distillation sheets Genome summary form: None Module step form: None ETC module database: None Function heatmap form: None AMG database: None (DRAM) [saraswati@hn1 DRAM_data]$ conda activate DRAM
Can you help me resolve this so that I can run DRAM to analyze my MAGs?
Thanks in Advance