kaichop
commented
2 years ago This is fine. The file is a region annotation file so idx is not required. The region is taken from published paper. The hg38 version is not available as the original publication only provides hg19/mm9. There is no update from the authors as far as I know.
On Fri, Jan 14, 2022 at 8:10 AM agarwalsurbhi @.***> wrote:
Dear Prof. Wang,
I am trying to download gerp++elem database for hg19 using command <perl annotate_variation.pl http://annotate_variation.pl -buildver hg19 -downdb -webfrom annovar gerp++elem humandb/>
which is producing the following error while downloading hg19_gerp++elem.txt.idx.gz file
NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_gerp++elem.txt.gz ... OK NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_gerp++elem.txt.idx.gz http://www.openbioinformatics.org/annovar/download/hg19_gerp++elem.txt.idx.gz ... Failed NOTICE: Uncompressing downloaded files NOTICE: Finished downloading annotation files for hg19 build version, with files saved at the 'humandb' directory WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg19_gerp++elem.txt.idx.gz http://www.openbioinformatics.org/annovar/download/hg19_gerp++elem.txt.idx.gz
Is hg19_gerp++elem.txt.idx.gz missing at the source? Is there another way possible to use this database? Also, the database was last updated in 2014. Are there any possibilities of new update?
Thanks! I will appreciate your help.
Surbhi
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agarwalsurbhi
Dear Prof. Wang,
I am trying to download gerp++elem database for hg19 using command <perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar gerp++elem humandb/>
which is producing the following error while downloading hg19_gerp++elem.txt.idx.gz file
NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_gerp++elem.txt.gz ... OK NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_gerp++elem.txt.idx.gz ... Failed** NOTICE: Uncompressing downloaded files NOTICE: Finished downloading annotation files for hg19 build version, with files saved at the 'humandb' directory WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg19_gerp++elem.txt.idx.gz**
Is hg19_gerp++elem.txt.idx.gz missing at the source? Is there another way possible to use this database? Also, the database was last updated in 2014. Are there any possibilities of new update?
Thanks! I will appreciate your help.
Surbhi