problem to download 1000genome database using ANNOVAR
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Entering edit mode
7.1 years ago
jan ▴ 170

I'm trying to annotate my VCF file using ANNOVAR function table_annovar.pl. There are few files that I need to download before I can use the function. I managed to download all the required files except for 1000 genomes database. Below is the command that I used.

annotate_variation.pl -buildver hg19 -downdb -webfrom annovar 1000g2014oct humandb/

However, I'm getting this error

NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done

NOTICE: Downloading annotation database http://www.openbioinformatics.... ... Done

NOTICE: Uncompressing downloaded files

[hg19_1000g2014oct.zip]

End-of-central-directory signature not found. Either this file is not

a zipfile, or it constitutes one disk of a multi-part archive. In the

latter case the central directory and zipfile comment will be found on

the last disk(s) of this archive.

note: hg19_1000g2014oct.zip may be a plain executable, not an archive

unzip: cannot find zipfile directory in one of hg19_1000g2014oct.zip or

hg19_1000g2014oct.zip.zip, and cannot find hg19_1000g2014oct.zip.ZIP, period.

NOTICE: Finished downloading annotation files for hg19 build version, with files saved at the '1000g' directory

I'm running my analysis on UNIX

annovar table_annovar.pl annotate_annovar.pl • 3.0k views
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0
Entering edit mode
6.8 years ago

Try this:

perl annotate_variation.pl -downdb -webfrom annovar --buildver hg19 1000g2014oct /humandb.

Maybe the file is corrupted. Try download again. If error persist then check your administrator to see what is happen with your system.

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