Hey Saatvik, I'm able to replicate your error here. The problem is our support for tracks of type "maf" don't support the use of the trackDb variable "mafFile" properly. A work-around for this problem is to make the type of your track "wigMaf" in the trackDb entry (see README in kent/src/hg/makeDb/trackDb for details).
I hope this resolves your error. If not, please respond to this message cc'ing the mail list. brian On Thu, Mar 18, 2010 at 2:48 AM, Saatvik Agarwal <[email protected]> wrote: > Hello, > > I am trying to display pairwise alignments generated by BLAT (Genbank > sequences to hg18) using the MAF format. I like the MAF format since it is > pretty close to the UCSC cgi custom track for blat results in that it shows > gaps and mismatches graphically. Now if I upload my MAF track (attached) as > a custom track, it works fine, but if I load it into our mysql database (we > run a personal browser mirror) using hgLoadMaf and add it to my trackDb.ra > entry it doesn't work properly. It looks fine when you're zoomed out but > when I zoom in (to the point where it would normally show the seq. ident > plot) the browser crashes and just gives me a completely blank webpage. It's > obviously this track because if I turn it off everything else works fine. > > Any thoughts on what I might be doing wrong? All the examples I saw in the > kent src doc were multiple alignments to reference genomes. My MAF aligns > short sequences from Genbank to a reference genome. > > My commands for loading the MAF looks like this: > > hgLoadMaf hg18 bejsaGenbankBLAT > -pathPrefix=/cluster/u/curator/tracks/hg18 -custom > -loadFile=genbankBLAT.maf > hgLoadMafSummary -minSize=50 -mergeGap=500 -maxSize=50000 hg18 > bejsaGenbankBLATSummary /cluster/u/curator/tracks/hg18/genbankBLAT.maf > > and my hg18 trackDb.ra entry is as follows: > > track bejsaGenbankBLAT > shortLabel Endogenous enhancers > longLabel Endogenous (same species) enhancers BLAT > color 0,255,0 > priority 1000 > group regulation > visibility dense > mafDot on > type maf > mafFile /cluster/u/curator/tracks/hg18/genbankBLAT.maf > summary bejsaGenbankBLATSummary > > Thanks, > Saatvik > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
