<html><head></head><body bgcolor="#FFFFFF"><div>Hello,</div><div><br></div><div>I'm ccing this to the gbrowse mailing list; the help list can be trimmed from future replies. </div><div><br></div><div>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:</div><div><br></div><div>chr1 . chromosome 1 12345678 . . . Name=chr1</div><div><br></div><div>You have to let gbrowse know what chr1 is.</div><div><br></div><div>Scott</div><div><br></div><div><br>Sent from my iPhone</div><div><br>On Feb 16, 2012, at 3:22 AM, huquanjun <<a href="mailto:huquanjun@gmail.com">huquanjun@gmail.com</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div><font class="Apple-style-span" size="4">Hi,</font><div> 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:</div><div><br></div><div><div><b>chr1<span class="Apple-tab-span" style="white-space:pre"> </span>pop1<span class="Apple-tab-span" style="white-space:pre"> </span>SNP<span class="Apple-tab-span" style="white-space:pre"> </span>111<span class="Apple-tab-span" style="white-space:pre"> </span>111<span class="Apple-tab-span" style="white-space:pre"> </span>99<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=id1;Name=snp1;</b></div><div><b>…</b></div></div><div> </div><div> and then loaded it into postgresql database with:</div><div><br></div><div><b> bp_seqfeature_load.pl -d 'dbi:Pg:dbname=db1' -a DBI::Pg -c -u user snp.gff3</b></div><div><b><br></b></div><div><b> </b> then gbrowse show: </div><div><br></div><div> <b>Gateway Time-out</b></div><div><b> The gateway did not receive a timely response
from the upstream server or application.</b></div><div><b><br></b></div><div> I checked debug logs:</div><div><b> </b></div><div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b>get_feature_by_name(-name chr_1* -class Clone -start 1484307 -end 1552071) => at /.../Browser2/Region.pm , </b></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b> get_features_by_alias(-name chr_1* -class Clone -start 1484307 -end 1552071) => at /.../Browser2/Region.pm ., </b></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b> get_features_by_alias(-name chr_1* -class Clone -start 1484307 -end 1552071) => at /.../Browser2/Region.pm ., </b></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b>Timeout waiting for output from CGI script /var/www2/cgi-bin/gbrowse/gbrowse,</b></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b> Script timed out before returning headers: gbrowse, </b></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b> Use of uninitialized value $argv[1] in join or string at /.../Browser2/Region.pm , </b></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b> get_feature_by_name(-name ) => SNP:pop1(id1) at /.../Browser2/Region.pm ., </b></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b> Use of uninitialized value $argv[1] in join or string at /...Browser2/Region.pm , </b></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b> get_features_by_alias(-name ) => SNP:pop1(id1) at /...Browser2/Region.pm </b></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b> segment => SNP:pop1(id1) at /.../Browser2/Region.pm </b></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b> Timeout waiting for output from CGI script /var/www2/cgi-bin/gbrowse/gbrowse,</b></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b><br></b></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b style="font-weight: bold; "> </b>but I don't know how to fix the problem</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; ">Thanks for help!</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><br></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><b><br></b></div><div style="font-weight: bold; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Droid Sans'; "><br></div></div></div></blockquote></body></html>