MAFs not rendering correct

[Jaaved Mohammed]

Hello,

I'm trying to debug a rendering problem I'm facing with the Cornell University mirror of the UCSC genome browser (http://genome-mirror.bscb.cornell.edu/). I've created two custom MAF tracks for Drosophila in addition the prebuilt 15-way Insect alignment. I've noticed that when I zoom into the base level of these custom MAFs, the alignment does not render correctly. In addition, the track content spills over into the next track (see attachment). When I zoom out to escape from the base level, the MAF is rendered correctly (see attachment). I've not observed the problem with the 15-way insect alignment, but only with my custom alignment. As far as I can tell, the only difference between my custom track configuration (in the trackDb.ra file) and that of the 15-way insect alignment is the mafFile argument:

track multiz20way
shortLabel Conservation 20way
longLabel 20 flies MULTIZ Alignments & phastCons Scores
group compGeno
priority 100
visibility dense
type wigMaf 0.0 1.0
maxHeightPixels 100:40:11
wiggle phastCons20way
yLineOnOff Off
autoScale Off
windowingFunction mean
summary multiz20waySummary
#frames multiz20wayFrames
irows on
speciesCodonDefault dm3
speciesOrder droSim2 droSec2 droYak3 droEre2 droEug1 droBia1 droTak1 droEle1 droRho1 droFic1 droKik1 droAna3 droBip1 dp5 droPer2 droWil2 droVir3 droMoj3 droGri2
mafFile /gbdb_cornell/dm3/multiz20way/maf/multiz20way.maf

If not sure if this mafFile argument has anything to do with this behavior...it's the only difference I could find. I should note that everything rendered properly about a month ago. Some recent build of the genome browser may have caused this problem. We just did a sync and build this morning with the latest and greatest version, but the problem still persists.

Any help is appreciated.

Thanks,
Jaaved

 

[Jonathan Casper]

Hello Jaaved,

Thank you for your question about the display of custom MAF tracks. One of our engineers is looking into this issue, but hasn't been able to reproduce the problem on your server (http://genome-mirror.bscb.cornell.edu/) using the dm3 assembly. Can you please send us a link to a saved session that shows the problem? Thanks!

If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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[Jaaved Mohammed]

Well that is very strange. I just confirmed that the problem does not repro on the main browser mirror site, but it does on my development browser at http://jm889.genome-mirror.bscb.cornell.edu.

Here is the session link:
http://jm889.genome-mirror.bscb.cornell.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=jaavedm&hgS_otherUserSessionName=dm3%2Dbasic

I'm not sure if you'll be prompted for a password when you access this session link. I know that some tracks on my dev browser is password protected. Let me know.

Thanks for helping me to debug this further.

-Jaaved

[Jonathan Casper]

Hello Jaaved,

It looks like your development server CGIs are password protected (not just the custom tracks - all of the CGIs are). Are you able to give us temporary access to it? Alternatively, are you able to create a track hub that also causes the problem on your live mirror and send us a link to that? You can reply to me privately to avoid sharing this with the mailing list.

If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

[Jaaved Mohammed]

Hello,

I'm checking in to see if there has been any update on this issue. We don't modify the source code once sync'ed. We have some custom databases that supplement the genomes on the original UCSC genome browser, but that is all on the mysql side. Let me know if I can help with debugging this further.

Thanks,
Jaaved

[Luvina Guruvadoo]

Hello Jaaved,

Unfortunately, we were unable to debug this since we couldn't reproduce it locally. I'm sorry we aren't able to provide any additional information at this time. We'll contact you if anything changes.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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