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.
>
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