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maximilianh / crisporWebsite

All source code of the crispor.org website
http://crispor.org
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Error while downloading hg38 data #14

Closed asgarhussain closed 5 years ago

asgarhussain commented 5 years ago

I am getting following error when I tried to download hg38 database using this command

sudo ./crisprAddGenome ucsc hg38

==== Downloading ensembl transcripts to gene name table ==== INFO:root:Running: wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ensemblToGeneName.txt.gz -O - | zcat > /tmp/hg38/hg38.ensemblToGeneName.txt --2018-07-27 17:41:30-- http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ensemblToGeneName.txt.gz Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. HTTP request sent, awaiting response... 404 Not Found 2018-07-27 17:41:32 ERROR 404: Not Found.

gzip: stdin: unexpected end of file Could not run command wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ensemblToGeneName.txt.gz -O - | zcat > /tmp/hg38/hg38.ensemblToGeneName.txt

UCSC has removed this file from URL.

maximilianh commented 5 years ago

Actually, for hg38, you wouldn't use this command at all. You would use the other tool, crisprGetGenome (or was it crisprDownloadGenome?). Anyhow, just use the other script. :-)

On Fri, Jul 27, 2018 at 3:01 PM, asgarhussain notifications@github.com wrote:

I am getting following error when I tried to download hg38 database using this command

sudo ./crisprAddGenome ucsc hg38

==== Downloading ensembl transcripts to gene name table ==== INFO:root:Running: wget http://hgdownload.cse.ucsc. edu/goldenPath/hg38/database/ensemblToGeneName.txt.gz -O - | zcat > /tmp/hg38/hg38.ensemblToGeneName.txt --2018-07-27 17:41:30-- http://hgdownload.cse.ucsc. edu/goldenPath/hg38/database/ensemblToGeneName.txt.gz Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. HTTP request sent, awaiting response... 404 Not Found 2018-07-27 17:41:32 ERROR 404: Not Found.

gzip: stdin: unexpected end of file Could not run command wget http://hgdownload.cse.ucsc. edu/goldenPath/hg38/database/ensemblToGeneName.txt.gz -O - | zcat > /tmp/hg38/hg38.ensemblToGeneName.txt

UCSC has removed this file from URL.

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asgarhussain commented 5 years ago

Thanks

maximilianh commented 5 years ago

did it work?

On Mon, Jul 30, 2018 at 12:16 PM, asgarhussain notifications@github.com wrote:

Thanks

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