IGV 2.4.4 crashing when I zoom in to view junctions on a bam file

[thewatson...@gmail.com]

Hi there,

Forgive me in advance, if I say something embarrassing, I'm new to genome viewing.

I am trying to look at splice junctions using .bam files aligned to the mouse genome. I can generally search genes ok but almost every time I either zoom to view junctions or grab and drag the viewer to view a different genomic locus, I get a blue spinning circle and the program freezes. 
I've downloaded every single different Mac file you offer, including all the different jnlps. It happens regardless of how I open the viewer.

My computer specs are:

MacOS High Sierra 10.13.1, 16GB 1600Mhz DDR3

I have Java 8.

Using IGV_2.4.4

I'm attaching my log file. 

Please let me know if you know why this freezing occurs!

Kristin

[James Robinson]

Thanks for the report, we will look into it.   Could I ask you to try reproducing the problem with public data we can access by following the instructions below?  It would help in determining the issue.

* Start IGV and select "Human hg19" as the genome.

* Select "File > Load from Server" and then load  "Body Map 2.0 > Alignments > Merged 50bp and 75bp > adipose

* Repeat the actions that cause the freezing of the mouse data

If you are able to reproduce it with this data please give us the steps you take with as much detail as possible.   If we can reproduce it we can fix it.

Also, you mention junctions,  I assume that means you have the junctions track enabled, correct?

Jim

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[Kristin Patrick]

Yep, my junction track is enabled!

Ok, so I followed your instructions and searched a gene (Actb). I pressed the plus button to zoom several times and when it got to the point where it was zoomed in enough to show me the junctions, there was a delay of several minutes-- it seemed frozen but the read numbers on the bottom of the window were slowly ticking up so I left it be and eventually it loaded. I had no problem moving around the locus with grab and drag on the window.

Then I searched another gene (Ifit1). Again, I used the + button to zoom into the junction level resolution and it got stuck after 1 or 2 clicks on +. Several minutes of swirling blue circle, I can't click anything in the IGV, there's no change in the reads loaded on the bottom right (stuck at 1.176M of 1.617M). 

Does that help?

K

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[James Robinson]

Yes, that's very helpful.   Could you also send another copy of your igv.log so I can see what was happening during this session?

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[Kristin Patrick]

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[James Robinson]

Thanks, but I don't see from the log that you loaded any body-map alignments,  rather it looks like you loaded an assembly.   Here's an easier way,  select "Human hg19"  then  "File > Load from URL" and paste in this url.  

 https://www.broadinstitute.org/igvdata/BodyMap/hg19/IlluminaHiSeq2000_BodySites/adipose_merged/accepted_hits.bam

Or if you prefer the menu 

​

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[Kristin Patrick]

Ok tried again.

Loaded Actb...took very long time (5 min?) to load reads-- tried to zoom into see the junction track more closely-- viewer froze, could not zoom at all.

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[James Robinson]

Have you changed any user preferences?  Please attach the prefs.properties file,  it is in the same folder as igv.log.    Reads from bodymap load for me in ~ 10 seconds.

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[Kristin Patrick]

I may have changed a couple things...see attached.

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[James Robinson]

OK,  yes, something has gone wrong on the 2.4 branch.   This was not reproducible with other genes I tried,  but certainly is with actb.

I tested on 2.3.98 (last of the 2.3 releases)  and its o.k.   I suggest you use that release until I find and correct the problem.    Note that the coverage on that gene is very deep,  almost a million reads,  so it does take some time to load.  For me 1 minute,  vs ~5 on the 2.4.4 release.

You can download the 2.3.98 release from here: http://data.broadinstitute.org/igv/projects/downloads/2.3/IGV_2.3.98.app.zip

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[James Robinson]

I think I have identified and fixed the issue.   This will be released this evening as 2.4.5.   Thank you for your patience.  

[James Robinson]

Hi, 

We just released v 2.4.5,  which has fixes and optimizations for very deep coverage bam files.   It should address the issues you were experiencing.    Please let us know if it does not.

Jim