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

[huquanjun]

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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