Snpeff run with downloaded genome database

Question

[ttom]

Hi,

I am trying to run SnpEff (version 4.4) and I have already downloaded the hg38 database and kept it locally

java -Xmx4g -jar snpEff.jar -c snpEff.config hg38 test_chr22.vcf >test_chr22.ann.vcf

hg38 Genome has been downloaded and kept in a local path and is given in the snpEff.config file data.dir = /cluster/software/snpEff/data/hg38

However, snpEff is still trying to connect to internet to download the Genome database. I am running it some where I do not have access to internet and hence the genome database is downloaded.

Error shown below

Picked up JAVA_TOOL_OPTIONS: -Xmx2g
00:00:00 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_hg38.zip
00:00:00 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_hg38.zip
FATAL ERROR: Failed to download database from [https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_hg38.zip, https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_hg38.zip

Answer 1

[GenoMax]

Add -nodownload -noLog to your command and see if that prevents the check.

[ttom]

It is working with the nodownload option along with, giving the path of local genome data repo in the config file

java -Xmx4g -jar snpEff.jar hg38 -nodownload test_chr22.vcf >test_chr22.ann.vcf