jiarong
commented
1 year ago Looks like an issue with DRAMv database. Try DRAM-setup.py update_description_db and see if it fixes the issue. See more details in this thread:
https://github.com/WrightonLabCSU/DRAM/issues/158
carmennns2
Hi, I am new to Virsorter2 and DRAMv.
When running DRAMv, I got this error:
DRAM-v.py annotate \ -i /scratch/hdd2/carmen/Metagenomics_16S/Phage/phage_annotation/test2.2/vs2/9968_vs2/for-dramv/final-viral-combined-for-dramv.fa \ -v /scratch/hdd2/carmen/Metagenomics_16S/Phage/phage_annotation/test2.2/vs2/9968_vs2/for-dramv/viral-affi-contigs-for-dramv.tab \ -o dramv-annotate --threads 30 --min_contig_size 1000
2022-09-29 12:28:51.428394: Viral annotation started 0:00:00.006462: Retrieved database locations and descriptions 0:00:00.006490: Annotating final-viral-combined-for-dramv 0:00:00.388120: Turning genes from prodigal to mmseqs2 db 0:00:02.223577: Getting hits from kofam 0:04:31.088310: Getting forward best hits from viral 0:04:31.747997: Getting reverse best hits from viral 0:04:32.318992: Getting descriptions of hits from viral /home/ca3226/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_009218533.1 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], Traceback (most recent call last): File "/home/ca3226/miniconda3/envs/DRAM/bin/DRAM-v.py", line 153, in
args.func(**args_dict)
File "/home/ca3226/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/ca3226/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/ca3226/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/ca3226/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/ca3226/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/ca3226/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_009218533.1'
Do you have any suggestions on how to resolve this issue?
Thank you so much! Carmen