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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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annotate_variation.pl fails to download files #196

Open cjyoon opened 2 years ago

cjyoon commented 2 years ago

I'm trying to download annovar database using the following command, but the download is not working. Could you help me troubleshoot?

$ perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar gnomad_genome humandb/  NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Failed
NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg38_gnomad_genome.txt.gz ... Failed
NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg38_gnomad_genome.txt.idx.gz ... Failed
WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg38_gnomad_genome.txt.idx.gz, http://www.openbioinformatics.org/annovar/download/hg38_gnomad_genome.txt.gz

$ perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar gnomad_genome humandb/
NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Failed
NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_gnomad_genome.txt.gz ... Failed
NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_gnomad_genome.txt.idx.gz ... Failed
WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg19_gnomad_genome.txt.idx.gz, http://www.openbioinformatics.org/annovar/download/hg19_gnomad_genome.txt.gz
kaichop commented 2 years ago

The file exists, you may need to switch to a different network to download or use a web browser to download the file. Some servers now block http file traffic, so you could try use "https" rather than "http" and then wget command manually. Also, you may want to use gnomad30 which is version 3.0 for genome data.

On Mon, Jun 20, 2022 at 12:49 PM Chris J Yoon @.***> wrote:

I'm trying to download annovar database using the following command, but the download is not working. Could you help me troubleshoot?

$ perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar gnomad_genome humandb/ NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg38_gnomad_genome.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg38_gnomad_genome.txt.idx.gz ... Failed WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg38_gnomad_genome.txt.idx.gz, http://www.openbioinformatics.org/annovar/download/hg38_gnomad_genome.txt.gz

$ perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar gnomad_genome humandb/ NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_gnomad_genome.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_gnomad_genome.txt.idx.gz ... Failed WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg19_gnomad_genome.txt.idx.gz, http://www.openbioinformatics.org/annovar/download/hg19_gnomad_genome.txt.gz

— Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/196, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OHPTUI4THTZT7JYQ3DVQCOIDANCNFSM5ZJQPDFQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

fengxiuming commented 2 years ago

I have the same question about this, however, I have succeed to download annovar database via a web browser. The .gz is large and it need some time. Then I have succeed to gzip -d the .gz file.

sahinsrhn commented 12 months ago

Hi, I got same error for gnomad v4 database. I try other options but unable to download gnomad40_genome dataset. On the other hand, i was able to download gnomad40_exome without a problem. I would happy if you can check that.

Thanks.

kaichop commented 12 months ago

gnomad40_genome will be updated later today.

On Mon, Nov 27, 2023 at 12:05 PM Şahin Sarıhan @.***> wrote:

Hi, I got same error for gnomad v4 database. I try other options but unable to download gnomad40_genome dataset. On the other hand, i was able to download gnomad40_exome without a problem. I would happy if you can check that.

Thanks.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/196#issuecomment-1828263436, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OGWMKABDQQLMXDNHSLYGTB6RAVCNFSM5ZJQPDF2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBSHAZDMMZUGM3A . You are receiving this because you commented.Message ID: @.***>

sahinsrhn commented 12 months ago

sorry didn't realize release day is today. Thanks