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tseemann / abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
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BLAST Database error: Error pre-fetching sequence data #164

Closed ramadatta closed 3 years ago

ramadatta commented 3 years ago

Hi,

I have installed abricate using conda. When I run the command:

$ abricate test.fasta
Using nucl database ncbi:  5386 sequences -  2021-Mar-27
#FILE   SEQUENCE    START   END STRAND  GENE    COVERAGE    COVERAGE_MAP    GAPS    %COVERAGE   %IDENTITY   DATABASE    ACCESSION   PRODUCT RESISTANCE
Processing: test.fasta
BLAST Database error: Error pre-fetching sequence data 
Found 0 genes in test.fasta
Tip: it's important to realise abricate uses DNA matching, not AA.
Done.

Can kindly request help on how to resolve this. Many thanks in advance.

lireo commented 3 years ago

Hi

I have same problem with a fresh abricate install with conda. Also, appreciate any help I can get

andersgs commented 3 years ago

Can you confirm the blast version? Thank you.

lireo commented 3 years ago

My blast version is : blastn: 2.9.0+ Package: blast 2.9.0, build Sep 26 2019 23:31:55

Thank you for your help

andersgs commented 3 years ago

The issue comes down to a change in the blast DB format. NCBI updated their default DB format from V4 to V5.

blast 2.9 was the last version that read (and wrote) V4 by default (optionally it would read/write V5). From version 2.11 (I believe) V4 support is dropped all together.

The current blast DB shipped with abricate is V5.

You have two options:

  1. Run abricate --setupdb which will re-create all the blast DBs. Since you have blast 2.9, it will do them in V4.

  2. Upgrade to blast v2.10 or above: conda install -c bioconda blast=2.11

I will work on the conda recipe to update the minimum requirements.

lireo commented 3 years ago

I can't update blast, there are to many conflicts but I succeed with your first solution abricate --setupdb

Thank you very much

andersgs commented 3 years ago

I will close this issue. If needed, please re-open.

ramadatta commented 3 years ago

abricate --setupdb resolved the issue. Thank you very much!

swati7024 commented 1 year ago

hey.. Even after updating the blast and also run the command abricate --setupdb my problem is not solved showing the same error blastN database not found... Also when I am creating the vfdb database it is extracting sequences in duplex, triplex and many more times... Please help.. Thank you