利用conda 下载的abricate ,其数据库版本较老
abricate --list DATABASE SEQUENCES DBTYPE DATE megares 6635 nucl 2021-Mar-27 resfinder 3077 nucl 2021-Mar-27 card 2631 nucl 2021-Mar-27 argannot 2223 nucl 2021-Mar-27 ecoh 597 nucl 2021-Mar-27 vfdb 2597 nucl 2021-Mar-27 plasmidfinder 460 nucl 2021-Mar-27 ecoli_vf 2701 nucl 2021-Mar-27 ncbi 5386 nucl 2021-Mar-27
为了用最新版，利用abricate自带的更新功能进行更新，出现了报错
abricate-get_db --db card --force Setting up 'card' in '/gpfs/home/huj/miniconda3/db/card' Downloading: https://card.mcmaster.ca/latest/data HTTP Result: 501 Destination: card.tar.bz2 Filesize: bytes tar: card.tar.bz2: Cannot open: No such file or directory tar: Error is not recoverable: exiting now ERROR: Problem with tar xf card.tar.bz2 ./card.json
后续通过安装 perl-lwp-protocol-https，解决了报错
conda install perl-lwp-protocol-https
再运行更新就没有了报错
abricate-get_db --db ncbi --force Setting up 'ncbi' in '/gpfs/home/huj/miniconda3/db/ncbi' Downloading: https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/AMR_CDS HTTP Result: 200 Destination: amr_cds.ffn Filesize: 8902716 bytes Downloading: https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ReferenceGeneCatalog.txt HTTP Result: 200 Destination: amr_cds.tsv Filesize: 1779953 bytes [amr_cds.tsv] Loaded 6770 records [amr_cds.ffn] 1 | blaLEN-42 | NG_066705.1 | class A beta-lactamase LEN-42 [amr_cds.ffn] 2 | blaTEM-156 | NG_050200.1 | class A beta-lactamase TEM-156 [amr_cds.ffn] 3 | blaPDC-114 | NG_055478.1 | class C beta-lactamase PDC-114 [amr_cds.ffn] 4 | blaPDC-226 | NG_056104.1 | class C beta-lactamase PDC-226 [amr_cds.ffn] 5 | blaPDC-116 | NG_055480.1 | class C beta-lactamase PDC-116 [amr_cds.ffn] 6 | blaPDC-298 | NG_060543.1 | class C beta-lactamase PDC-298
最好再检查是否更新完成，可以看到ncbi 数据库已经更新到2023
abricate --list DATABASE SEQUENCES DBTYPE DATE megares 6635 nucl 2021-Mar-27 resfinder 3077 nucl 2021-Mar-27 card 2631 nucl 2021-Mar-27 argannot 2223 nucl 2021-Mar-27 ecoh 597 nucl 2021-Mar-27 vfdb 2597 nucl 2021-Mar-27 plasmidfinder 460 nucl 2021-Mar-27 ecoli_vf 2701 nucl 2021-Mar-27 ncbi 6613 nucl 2023-Jul-24
以上就是更新abricate 数据库报错时候的解决方法，希望对大家有帮助