problems updating the database

[andrenalina1]

Hello

Before starting to update, the program indicated the following message (when I ran abricate --list): DATABASE SEQUENCES DB TYPE DATE ecoh 597 nucl 2018-Oct-20 ncbi 4579 nucl 2018-Oct-20 vfdb 2597 nucl 2018-Oct-20 card 2237 nucl 2018-Oct-20 resfinder 3021 nucl 2018-Oct-20 argannot 1749 nucl 2018-Oct-20 ecoli_vf 2701 nucl 2018-Oct-20 plasmidfinder 263 nucl 2018-Oct-20

But, when I have tried to update the database, I obtained the following error: BLAST options error: ... / abricate / db / ncbi / sequences is empty.

To update, I first used the command: abricate-get_db --db ncbi. When this didn't work, I tried with abricate-get_db --db ncbi --force. In both cases I had the same error message.

A clarification, I have version 0.8.10 installed, within a conda environment/linux system.

Sorry if my question is very elemental, but I'm a bit new to bioinformatics.

[omrctnr]

Hi,

I had a similar problem with you. The databases were on 2017 in terms of me (abricate --list).

I also checked _miniconda/bin/abricate and abricate-getdb files' date and It belonged to 2018.

The problem was solved as follows: conda update -c conda-forge -c bioconda -c defaults abricate

If it works, be sure to update all databases abricate --setupdb

abricate --list

megares 6635    nucl    2021-Aug-26
resfinder       3077    nucl    2021-Aug-26
card    2631    nucl    2021-Aug-26
argannot        2223    nucl    2021-Aug-26
ecoh    597     nucl    2021-Aug-26
vfdb    2597    nucl    2021-Aug-26
plasmidfinder   460     nucl    2021-Aug-26
ecoli_vf        2701    nucl    2021-Aug-26
ncbi    5386    nucl    2021-Aug-26

abricate --version abricate 1.0.1

Hopefully, the solution will be useful to you. Omer

[drelo]

Thanks @omrctnr it worked like charm in my case

[m-ocejo]

Dear @omrctnr, I used the solution you posted. However I realized that the database is still not updated, I guess the abricate --setupdb only sets up the database without updating it first.

In my case, (abricate v.1.0.1 blastn: 2.12.0+) on Ubuntu 20.04.3 LTS, the output was:

abricate-get_db --force -db ncbi

Setting up 'ncbi' in '/home/labsani/miniconda3/envs/abricate/db/ncbi' Downloading: https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/AMR_CDS HTTP Result: 501 Destination: amr_cds.ffn Filesize: bytes Downloading: https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ReferenceGeneCatalog.txt HTTP Result: 501 Destination: amr_cds.tsv Filesize: bytes ERROR: Can't read TSV file: amr_cds.tsv

Am I missing something?

[theadrija]

@m-ocejo Hi! Were you able to solve the issue?