On 11/19/10 8:33 PM, Hiram Clawson wrote: > Take a look in your Apache error log files to see if there > are any error messages about your track from the browser CGI > binaries. The messages should have appeared when you loaded > the tracks, but maybe something else is going wrong.
Hi Hiram, our admin got back to us with the following error in apache log: [Mon Nov 22 16:00:02 2010] [error] invalid block header [Mon Nov 22 16:00:02 2010] [error] got -1 from read_block Is it something that is helpful at all? Thanks, D. > --Hiram > > ----- Original Message ----- > From: "Duke"<[email protected]> > To: [email protected] > Sent: Friday, November 19, 2010 5:11:32 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] empty data for BAM tracks > > Hi all, > > I just uploaded some of our new data to our local UCSC mirror (which is > locally accessible only). The data is in BAM format, and is hosted in > another server locally which, again is visible only locally (so > unfortunately I can not test the same BAM files with UCSC Browser). The > problem is I can not see any data in the track, just blank. There are > two points: > - Our local mirror works fine with other dataset (in BAM format) > - The pipeline analysis we use (to produce BAM) using samtools, and > all other dataset we have run also use the same pipeline > That means there is no difference between this BAM dataset and other > dataset we have done so far. I also use samtools to view the BAM files, > and they look fine to me. > > So any body has idea why this suddenly happened? What "quick and easy" > things should we do to debug the situation before we upload our BAM > files to somewhere outside to test with the real UCSC? > > Thank you very much, > > D. > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
