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dbSNP vcf file is corrupted?

Hi,

I downloaded the file 00-All.vcf.gz from https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/ by using the wget command:

wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/00-All.vcf.gz

When I try to gunzip the file:

gunzip -k 00-All.vcf.gz

I get the error:

gzip: 00-All.vcf.gz: invalid compressed data--crc error
gzip: 00-All.vcf.gz: invalid compressed data--length error

I tried to redownload but the problem persists.

Any thoughts on how to solve this?

Hadas

vcf gunzip dbsnp
• 3,432 views • link
written by HB • HB

works on my machine.

~$ wget -O - "http://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/00-All.vcf.gz" | gunzip -t && echo SUCCESS
URL transformed to HTTPS due to an HSTS policy
--2021-05-10 08:39:47--  https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/00-All.vcf.gz
Resolving cache.ha.univ-nantes.fr (cache.ha.univ-nantes.fr)... 193.52.104.20, 2001:660:7220:386:193:52:104:20
Connecting to cache.ha.univ-nantes.fr (cache.ha.univ-nantes.fr)|193.52.104.20|:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 16336802611 (15G) [application/x-gzip]
Saving to: ‘STDOUT’

-                                    100%[=====================================================================>]  15,21G  11,2MB/s    in 26m 47s 

2021-05-10 09:06:35 (9,69 MB/s) - written to stdout [16336802611/16336802611]

SUCCESS
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum 
wget https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/00-All.vcf.gz

and

gunzip 00-All.vcf.gz

also worked fine on my machine.

• 0 views • link
written by PKW • PKW

Thanks, I changed the prefix of the link from ftp:// to https:// and it worked!

• 0 views • link
written by HB • HB

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