Re: [Vcftools-help] tabix

[Petr D. <pd...@sa...>]

Hi,

tabix was giving this confusing message when querying remote files on
some systems. This should be fixed in latest SVN. If you give -f option,
it should run OK. 


On Thu, 2011-09-29 at 13:11 +0530, Neeba Dijo wrote:
> I installed tabix
>  
> and run the command
>  
> tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1...notypes.vcf.gz
> 1:233411980-245804116 > myfile.vcf 
> 
>  
> got an error
>  
> the index file is older than the vcf file. Please use '-f' to
> overwrite or reindex.
> 
>  
> and when running the command
>  
> 
> tabix -h ALL.chr1.phase1.projectConsensus.genotypes.vcf.gz | perl
> vcf-subset -c NA19240| bgzip
> -c /home/snagpal/NA19240.chr1.genotypes.vcf.gz
>  
> failed to open the file:
> ALL.chr1.phase1.projectConsensus.genotypes.vcf.gz
> [tabix] was bgzip used to compress this file?
> ALL.chr1.phase1.projectConsensus.genotypes.vcf.gz
> Can't open perl script "vcf-subset": No such file or directory

I think you forgot to redirect your output '> /home/.../file.vcf.gz'.

Best,
Petr

> 
>  
> Please help me to resolve the issue
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________ Vcftools-help mailing list Vcf...@li... https://lists.sourceforge.net/lists/listinfo/vcftools-help




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.