Failure to load alignment

[mtr...@mindspring.com]

Hello

I am having a strange problem.  I recently upgraded to IGV 2.3.88 (which solves an earlier problem I was having).  I have a process which generates an alignment (bam file) and associated tracks (bedgraph files).  It then creates a session file on our server which I then load into IGV via a link.  This was working fine up until yesterday.  Now when I click on the session file link, IGV opens the bedgraph files but not the bam file.  It indicates it is still loading but not never does.  If I try to load the bam file directly or via the url, a track is loaded but it is empty.  If I perform the original session file upload on another computer that has v2.3.88 installed, it works as expected.  If I download and reinstall IGV (either v2.3.88 or 2.3.86) on the problematic computer, the problem persists.  I would very much appreciate some help with this and it would be great if it would come today as, of course, I am suppose to be rolling out the tool that uses this to users tomorrow.  Isn't that always the way?

Much Thanks

Mark

[James Robinson]

Could you attach your igv.log file,  also your prefs.properties file,  both in your "igv" folder under your home directory.   Also, attaching the problematic session file might be helpful.

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[mtr...@mindspring.com]

As requested

Thanks for the help

On Thursday, November 17, 2016 at 11:20:24 AM UTC-5, Jim Robinson wrote:

Could you attach your igv.log file,  also your prefs.properties file,  both in your "igv" folder under your home directory.   Also, attaching the problematic session file might be helpful.

On Thu, Nov 17, 2016 at 5:08 AM, <mtr...@mindspring.com> wrote:

Hello

I am having a strange problem.  I recently upgraded to IGV 2.3.88 (which solves an earlier problem I was having).  I have a process which generates an alignment (bam file) and associated tracks (bedgraph files).  It then creates a session file on our server which I then load into IGV via a link.  This was working fine up until yesterday.  Now when I click on the session file link, IGV opens the bedgraph files but not the bam file.  It indicates it is still loading but not never does.  If I try to load the bam file directly or via the url, a track is loaded but it is empty.  If I perform the original session file upload on another computer that has v2.3.88 installed, it works as expected.  If I download and reinstall IGV (either v2.3.88 or 2.3.86) on the problematic computer, the problem persists.  I would very much appreciate some help with this and it would be great if it would come today as, of course, I am suppose to be rolling out the tool that uses this to users tomorrow.  Isn't that always the way?

Much Thanks

Mark

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[James Robinson]

Have you verified that it works in the previous version?  It would be helpful to know if the problem is with 2.3.88.   You can install the previous version from here,  if you don't still have it:  http://data.broadinstitute.org/igv/projects/downloads/IGV_2.3.87.exe

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