Hello Saatvik, Would you please send the following to help with our analysis:
1) Error messages (if any) from the time period when the problem occurred from /usr/local/apache/logs/error_log file (or the equivalent on your system). 2) A sample of your MAF data, the smallest sized file that you can create that still produces the display problem. If the file is still large, if you could gzip it and place it on a server where we could retrieve it (http or ftp w/ access instructions), that would be great. Please email the file or retrieval instructions directly to me, not to the entire list. The original MAF attachment was stripped by our mail screening program. Thank you! Jennifer On 3/18/10 2:48 AM, Saatvik Agarwal 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
