ANNOVAR Download Failing
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Entering edit mode
12 weeks ago
tony • 0

Wondering if anyone else is running into this issue. I am attempting to download some tables from ANNOVAR for variant annotation. However, every download command I make results in a failed attempt. I have a bash script that reads:

#!/bin/bash
# Command 1
perl annotate_variation.pl -webfrom annovar -downdb -buildver hg38 clinvar_20221231 humandb/

# Command 2
perl annotate_variation.pl -webfrom annovar -downdb -buildver hg38 refGeneWithVer humandb/

# Command 3
perl annotate_variation.pl -webfrom annovar -downdb -buildver hg38 knownGene humandb/

# Command 4
perl annotate_variation.pl -webfrom annovar -downdb -buildver hg38 ensGene41 humandb/

With the outcome failing with all attempts:

 (base) usr@usr-desktop:~/Desktop/yourmountingpoint/annovar$ source download.sh
 NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Failed
 NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg38_clinvar_20221231.txt.gz ... Failed
 NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg38_clinvar_20221231.txt.idx.gz ... Failed
 WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg38_clinvar_20221231.txt.gz, http://www.openbioinformatics.org/annovar/download/hg38_clinvar_20221231.txt.idx.gz

This is also the case when running

perl annotate_variation.pl -webfrom annovar -downdb avdblist -buildver hg38 .

Is anyone else having issues with the website; it could be down but did not see anything on their github issues regarding this.

ANNOVAR • 309 views
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