Hi Angie, No, I dont use KNETFILE_HOOKS and I believe our local mirror was not built with that option as well. But our samtools and mirror have been working just fine until I encouter that issue. I am gonna apply that patch and rebuild our samtools, but does that mean we have to ask our local admin to recompile (or apply batch) to the genome code as well?
Thanks, D. On 11/22/10 11:43 AM, Angie Hinrichs wrote: > Hi Duke, > > Did you compile your samtools and kent/src with KNETFILE_HOOKS=1 ? (That > requires downloading and applying a patch to the samtools source, see > http://genomewiki.ucsc.edu/index.php/KNETFILE_HOOKS .) If so, is it possible > to make a small test file that has the same problem, and put it on a public > site or email to me for debugging? > > If you didn't use KNETFILE_HOOKS, then empty bam track can be caused by stale > index files (.bam.bai) that the samtools C library saves in a local > directory. To clear all index files, "rm ${TRASHDIR}/samtools/*.bai" . > Depending on your installation, TRASHDIR is probably something like > /usr/local/apache/trash . If the track is still blank after clearing the > index files, please send a test case, or try "samtools view my.bam chr1:2-3" > where chr1:2-3 is the region you are viewing in the browser. > > Hope that helps, > Angie > > ----- "Duke"<[email protected]> wrote: > >> From: "Duke"<[email protected]> >> To: "Hiram Clawson"<[email protected]> >> Cc: [email protected] >> Sent: Saturday, November 20, 2010 6:08:56 AM GMT -08:00 US/Canada Pacific >> Subject: Re: [Genome] empty data for BAM tracks >> >> 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. >> Thanks Hiram for your suggestion. I have contacted our local admin about >> that. Aside from the admin side, based on your experience, is there any >> other reason from the user side that can cause the issue? >> >> Thanks, >> >> D. >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
