are they connected to the problems I met? like these
(DRAM) cat slurm-758068.out
/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_handler.py:81: UserWarning: No descriptions were found for your id's. Does this YP_003986888.1 look like an id from viral_description
warnings.warn("No descriptions were found for your id's. Does this %s look like an id from %s" % (list(ids)[0],
2022-10-29 12:27:54.183767: Viral annotation started
0:00:00.076933: Retrieved database locations and descriptions
0:00:00.076990: Annotating final-viral-combined-for-dramv
0:00:04.742257: Turning genes from prodigal to mmseqs2 db
0:00:06.192672: Getting hits from kofam
0:28:01.761758: Getting forward best hits from viral
0:28:09.242586: Getting reverse best hits from viral
0:28:15.722777: Getting descriptions of hits from viral
Traceback (most recent call last):
File "/home/zlinbz/miniconda3/envs/DRAM/bin/DRAM-v.py", line 153, in
args.func(**args_dict)
File "/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/annotate_vgfs.py", line 475, in annotate_vgfs
annotations = annotate_fastas(contig_locs, output_dir, db_handler, min_contig_size, prodigal_mode, trans_table,
File "/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/annotate_bins.py", line 1013, in annotate_fastas
annotate_fasta(fasta_loc, fasta_name, fasta_dir, db_handler, min_contig_size, prodigal_mode, trans_table,
File "/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/annotate_bins.py", line 921, in annotate_fasta
annotations = annotate_orfs(gene_faa, db_handler, tmp_dir, start_time, custom_db_locs, custom_hmm_locs,
File "/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/annotate_bins.py", line 814, in annotate_orfs
annotation_list.append(do_blast_style_search(query_db, db_handler.db_locs['viral'], tmp_dir,
File "/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/annotate_bins.py", line 684, in do_blast_style_search
hits = formater(hits, header_dict)
File "/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/annotate_bins.py", line 173, in get_basic_description
header = header_dict[hit]
KeyError: 'YP_003986888.1'
I don't know whether I have successfully set up the dram database. I used the command: DRAM-setup.py print_config, and got the result.
Processed search databases KEGG db: None KOfam db: /scratch/PI/boqianpy/App/DRAM_data/kofam_profiles.hmm KOfam KO list: /scratch/PI/boqianpy/App/DRAM_data/kofam_ko_list.tsv UniRef db: /scratch/PI/boqianpy/App/DRAM_data/uniref90.20221026.mmsdb Pfam db: /scratch/PI/boqianpy/App/DRAM_data/pfam.mmspro dbCAN db: /scratch/PI/boqianpy/App/DRAM_data/dbCAN-HMMdb-V10.txt RefSeq Viral db: /scratch/PI/boqianpy/App/DRAM_data/refseq_viral.20221029.mmsdb MEROPS peptidase db: /scratch/PI/boqianpy/App/DRAM_data/peptidases.20221029.mmsdb VOGDB db: /scratch/PI/boqianpy/App/DRAM_data/vog_latest_hmms.txt
Descriptions of search database entries Pfam hmm dat: /scratch/PI/boqianpy/App/DRAM_data/Pfam-A.hmm.dat.gz dbCAN family activities: /scratch/PI/boqianpy/App/DRAM_data/CAZyDB.07292021.fam-activities.txt VOG annotations: /scratch/PI/boqianpy/App/DRAM_data/vog_annotations_latest.tsv.gz
Description db: /scratch/PI/boqianpy/App/DRAM_data/description_db.sqlite
DRAM distillation sheets Genome summary form: /scratch/PI/boqianpy/App/DRAM_data/genome_summary_form.20221029.tsv Module step form: /scratch/PI/boqianpy/App/DRAM_data/module_step_form.20221029.tsv ETC module database: /scratch/PI/boqianpy/App/DRAM_data/etc_mdoule_database.20221029.tsv Function heatmap form: /scratch/PI/boqianpy/App/DRAM_data/function_heatmap_form.20221029.tsv AMG database: /scratch/PI/boqianpy/App/DRAM_data/amg_database.20221029.tsv
are they connected to the problems I met? like these (DRAM) cat slurm-758068.out /home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_handler.py:81: UserWarning: No descriptions were found for your id's. Does this YP_003986888.1 look like an id from viral_description warnings.warn("No descriptions were found for your id's. Does this %s look like an id from %s" % (list(ids)[0], 2022-10-29 12:27:54.183767: Viral annotation started 0:00:00.076933: Retrieved database locations and descriptions 0:00:00.076990: Annotating final-viral-combined-for-dramv 0:00:04.742257: Turning genes from prodigal to mmseqs2 db 0:00:06.192672: Getting hits from kofam 0:28:01.761758: Getting forward best hits from viral 0:28:09.242586: Getting reverse best hits from viral 0:28:15.722777: Getting descriptions of hits from viral Traceback (most recent call last): File "/home/zlinbz/miniconda3/envs/DRAM/bin/DRAM-v.py", line 153, in
args.func(**args_dict)
File "/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/annotate_vgfs.py", line 475, in annotate_vgfs
annotations = annotate_fastas(contig_locs, output_dir, db_handler, min_contig_size, prodigal_mode, trans_table,
File "/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/annotate_bins.py", line 1013, in annotate_fastas
annotate_fasta(fasta_loc, fasta_name, fasta_dir, db_handler, min_contig_size, prodigal_mode, trans_table,
File "/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/annotate_bins.py", line 921, in annotate_fasta
annotations = annotate_orfs(gene_faa, db_handler, tmp_dir, start_time, custom_db_locs, custom_hmm_locs,
File "/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/annotate_bins.py", line 814, in annotate_orfs
annotation_list.append(do_blast_style_search(query_db, db_handler.db_locs['viral'], tmp_dir,
File "/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/annotate_bins.py", line 684, in do_blast_style_search
hits = formater(hits, header_dict)
File "/home/zlinbz/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/annotate_bins.py", line 173, in get_basic_description
header = header_dict[hit]
KeyError: 'YP_003986888.1'