[Gmod-help] Problems about load millions of SNPs into database (GBrowse)

[Scott Cain]

Hello,

I'm ccing this to the gbrowse mailing list; the help list can be trimmed from future replies. 

From your error log, it looks like GBrowse is having a hard time finding chr1. Did you also load a GFF file that contained you reference sequences, that looked something like this:

chr1  .  chromosome   1   12345678   .   .   .   Name=chr1

You have to let gbrowse know what chr1 is.

Scott


Sent from my iPhone

On Feb 16, 2012, at 3:22 AM, huquanjun <huquanjun at gmail.com> wrote:

> Hi,
>    I have a working gbrowse, it display genes fine , but when I generated a gff3 file (contains only snp, and the file has 1900000 lines) looks like:
> 
> chr1	pop1	SNP	111	111	99	.	.	ID=id1;Name=snp1;
> …
>  
>   and then loaded it into postgresql database with:
> 
>   bp_seqfeature_load.pl -d 'dbi:Pg:dbname=db1' -a DBI::Pg -c -u user snp.gff3
> 
>   then gbrowse show: 
> 
>   Gateway Time-out
>   The gateway did not receive a timely response from the upstream server or application.
> 
>   I checked debug logs:
>   
> get_feature_by_name(-name chr_1* -class Clone -start 1484307 -end 1552071) =>  at /.../Browser2/Region.pm , 
>  get_features_by_alias(-name chr_1* -class Clone -start 1484307 -end 1552071) =>  at /.../Browser2/Region.pm ., 
>  get_features_by_alias(-name chr_1* -class Clone -start 1484307 -end 1552071) =>  at /.../Browser2/Region.pm ., 
> Timeout waiting for output from CGI script /var/www2/cgi-bin/gbrowse/gbrowse,
>  Script timed out before returning headers: gbrowse, 
>  Use of uninitialized value $argv[1] in join or string at /.../Browser2/Region.pm , 
>  get_feature_by_name(-name ) => SNP:pop1(id1) at /.../Browser2/Region.pm ., 
>  Use of uninitialized value $argv[1] in join or string at /...Browser2/Region.pm , 
>  get_features_by_alias(-name ) => SNP:pop1(id1) at /...Browser2/Region.pm 
>  segment => SNP:pop1(id1) at /.../Browser2/Region.pm 
>  Timeout waiting for output from CGI script /var/www2/cgi-bin/gbrowse/gbrowse,
> 
>   but I don't know how to fix the problem
> 
> Thanks for help!
> 
> 
> 
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