[Gmod-gbrowse] 80 millions SNPs, track rendering error, timeout, try viewing a smaller region

[Aimin Li]

Hi, everyone,
I loaded about 80 millions SNPs into GBrowse 2.55. I can view a SNP or a small region (100bp) on gbrowse.
However, it failed when viewing about 500bp or 1kbp region. The following is what I tested and configuration.

#======================
# TEST :
WEBSITE:
http://res.xaut.edu.cn/cgi-bin/gb2_dspsp/gbrowse/dspsp/

error,failed:
1:13,026,145..13,026,244
http://res.xaut.edu.cn/cgi-bin/gb2_dspsp/gbrowse/dspsp/?name=NUGGC

success:
1:82,234..82,534
http://res.xaut.edu.cn/cgi-bin/gb2_dspsp/gbrowse/dspsp/?name=SSCrs01000011459

#======================
# gff3: ( about 80,000,000 rows/features)
1 dspsp_general SNP 12867 12867 . + . ID=SSCrs01000012867;Name=SSCrs01000012867;Ref=T;Alt=G;dbSNPid=.
1 dspsp_general SNP 12894 12894 . + . ID=SSCrs01000012894;Name=SSCrs01000012894;Ref=A;Alt=C;dbSNPid=.
1 dspsp_general SNP 26956 26956 . + . ID=SSCrs01000026956;Name=SSCrs01000026956;Ref=C;Alt=G;dbSNPid=.
1 dspsp_general SNP 42241 42241 . + . ID=SSCrs01000042241;Name=SSCrs01000042241;Ref=T;Alt=G;dbSNPid=.
1 dspsp_general SNP 53053 53053 . + . ID=SSCrs01000053053;Name=SSCrs01000053053;Ref=T;Alt=A;dbSNPid=.
1 dspsp_general SNP 72646 72646 . + . ID=SSCrs01000072646;Name=SSCrs01000072646;Ref=A;Alt=G;dbSNPid=.
1 dspsp_general SNP 76467 76467 . + . ID=SSCrs01000076467;Name=SSCrs01000076467;Ref=T;Alt=A;dbSNPid=rs340612171
1 dspsp_general SNP 76469 76469 . + . ID=SSCrs01000076469;Name=SSCrs01000076469;Ref=A;Alt=C;dbSNPid=rs322594773

#======================
# config:
[dspsp_outgroup]
feature = SNP:dspsp_outgroup
glyph = triangle
point = 1
orient = N
height = 6
bgcolor = blue
fgcolor = blue
key = SNPs (outgroup)
category = SNP

[dspsp_general]
feature = SNP:dspsp_general
glyph = triangle
point = 1
orient = N
height = 6
bgcolor = blue
fgcolor = blue
key = SNPs (general)
category = SNP

#======================
# gbrowse.config:
slave_timeout =200
global_timeout =300
search_timeout =200

Thanks a lot!



Best wishes,
Mr Aimin Li
School of Computer Science and Technology,
Xidian University, Xi'an, China