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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Downloading annotation database ....Failed #237

Open Acetyl-ZHOU opened 10 months ago

Acetyl-ZHOU commented 10 months ago

I want to get gnomad211,and I runannotate_variation.pl -downdb gnomad211 humandb -buildver hg19 but NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gnomad211.txt.gz ... Failed WARNING: Some files cannot be downloaded, including http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gnomad211.txt.gz

can you give me some help?

kaichop commented 10 months ago

You can add '-webfrom annovar' to the command line.

On Thu, Jan 4, 2024 at 7:26 AM Acetyl-ZHOU @.***> wrote:

I want to get gnomad211,and I runannotate_variation.pl -downdb gnomad211 humandb -buildver hg19 but NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gnomad211.txt.gz ... Failed WARNING: Some files cannot be downloaded, including http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gnomad211.txt.gz

can you give me some help?

— Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/237, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OH4PWJ6WKUHPCNPLTDYM2NYTAVCNFSM6AAAAABBM3HFGOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3DKNJXGE4TONA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

mdanzi commented 9 months ago

Hello, I am also having this issue and wanted to mention that I think it is because UCSC changed their path from 'hgdownload.cse.ucsc.edu' to 'hgdownload.soe.cse.ucsc.edu'. While I acknowledge that your solution also works for many files, could you potentially update Annovar to look in this new location?

kaichop commented 9 months ago

That particular file for gnomad is compiled and provided in annovar, which is why the '-webfrom annovar' is needed. For UCSC provided files, I will update annovar to look into this new location; also a user-specified URL can be provided in the command line as a temporary fix.

On Wed, Feb 7, 2024 at 1:44 PM mdanzi @.***> wrote:

Hello, I am also having this issue and wanted to mention that I think it is because UCSC changed their path from 'hgdownload.cse.ucsc.edu' to ' hgdownload.soe.cse.ucsc.edu'. While I acknowledge that your solution also works for many files, could you potentially update Annovar to look in this new location?

— Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/237#issuecomment-1932657910, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3ODDH6AUK62PGKXL2BTYSPDRFAVCNFSM6AAAAABBM3HFGOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZSGY2TOOJRGA . You are receiving this because you commented.Message ID: @.***>

mdanzi commented 9 months ago

Thanks! I'll try the user-specified URL approach in the meantime. I didn't know about that.