abricate 升级数据库报错解决方案

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