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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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UserWarning: No descriptions were found for your id's. Does this YP_009966079.1 look like an id from viral_description #183

Closed qinjunjun closed 2 years ago

qinjunjun commented 2 years ago

Thank you for this useful tool,I met a little bug. This is my command line: DRAM-v.py annotate -i final-viral-combined-for-dramv.fa -v viral-affi-contigs-for-dramv.tab -o annotation_out 2022-06-04 18:40:33.748248: Viral annotation started 0:00:00.919200: Retrieved database locations and descriptions 0:00:00.919291: Annotating final-viral-combined-for-dramv 0:04:01.753534: Turning genes from prodigal to mmseqs2 db 0:04:18.797350: Getting hits from kofam 1:36:31.475152: Getting forward best hits from viral 1:37:19.089543: Getting reverse best hits from viral 1:37:29.686614: Getting descriptions of hits from viral /data1/qinjunjun/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_009966079.1 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 "/data1/qinjunjun/miniconda3/envs/dram/bin/DRAM-v.py", line 153, in args.func(**args_dict) File "/data1/qinjunjun/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 "/data1/qinjunjun/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 "/data1/qinjunjun/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 "/data1/qinjunjun/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 "/data1/qinjunjun/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 "/data1/qinjunjun/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_009966079.1'

can you help me? Thank you a lot.

rmFlynn commented 2 years ago

This is a reoccurring issue, example, sometime setup does not finish correctly. This is usually solved by running DRAM-setup.py update_description_db let me know if that does not work for you and I will figure out the problem.

qinjunjun commented 2 years ago

This is a reoccurring issue, example, sometime setup does not finish correctly. This is usually solved by running DRAM-setup.py update_description_db let me know if that does not work for you and I will figure out the problem.

Thank you ,I will try your way .

qinjunjun commented 2 years ago

This is a reoccurring issue, example, sometime setup does not finish correctly. This is usually solved by running DRAM-setup.py update_description_db let me know if that does not work for you and I will figure out the problem.

Thank you a lot ,now it works well.

rmFlynn commented 2 years ago

Glad to here it!