Issue with PLASMID download?

[axemango]

HI there,

while tying to compile the standard database or a custom database with plasmid I receive the error:

gzip: plasmid.1.1.genomic.fna.gz: invalid compressed data--format violated

Should this be downloading from the below location or another section of the NCBI ftp? I don't see plasmid listed here.

ftp.ncbi.nlm.nih.gov/genomes/refseq/

Kind regards
Axe

[SergeyBaikal]

Haven't you solved the problem?

[bsenf27]

I'v got the same error - two year later, command "kraken-build --standard ..."

gzip: plasmid.1.1.genomic.fna.gz: invalid compressed data--format violated
gzip: plasmid.2.1.genomic.fna.gz: invalid compressed data--format violated
gzip: plasmid.3.1.genomic.fna.gz: invalid compressed data--format violated
gzip: plasmid.4.1.genomic.fna.gz: invalid compressed data--format violated
gzip: plasmid.5.1.genomic.fna.gz: invalid compressed data--format violated

Bernd S.

[quliping]

Hello everyone, I found the method to solve this problem:
DerrickWood/kraken2#515 (comment)
You can try this, and it's worked for me, and here is an example for the path of the script file which need to be modified:
/public/apps/anaconda/envs/kraken2/share/kraken2-2.1.3-1/libexec/download_genomic_library.sh