Can't get IGV to work for me
jnic...@uvm.edu
I have a laptop running 32bit, Windows 7, with 3Gb of memory, JAVA 8 update 73, 34GB free harddrive space
I am trying to work with bam files of mtDNA sequence (~16,500 bp) with 3 to 7 million reads of 150 bp (coverage ~29,000x). File sizes are 240,000 to 500,000KB.
I installed the Launch with 1.2GB version 2.3 and it installed great but won’t complete loading most of the files. Up to about 330,000KB work but the rest give a “memory is low, reading terminating”. When I click OK, it gives me like 75 to 95% of the sequence.
So I tried the Download Windows package. When I clicked the IGV.bat, it got a quick glance of a DOS window which disappeared. When I loaded it from a DOS prompt, I got the following: This version of …IGV_2.3.69_jre\jre1.8.0_72\bin\javaw.exe is not compatible with the version of Windows you’re running. Check your computer’s system information to see whether you need a x86 (32-bit) or x64 (64-bit) version of the program, and then contact the software publisher.
I have attached igv.log but don't know which attempt it is from.
So any suggestions on how to get either version to work on my laptop? Can I adjust the settings on the Launch 1.2 so it uses less memory? I gather it may be set for large sequence and low copy number? which is just the opposite of what I have. And there are 3 tracks, one for splicing which obviously is irrelevant for mtDNA. Can I dump that track to save memory? Or should I just give up on my 32bit laptop and try to find a friend with a 64bit machine?
Thanks! Jan Nicklas
Jim Robinson
You probably not be able to load those without 64 bit windows, the 1.2 GB version has limited memory. You might try the 2 GB version, it might start or might not, technically it shouldn't work on 32 bit windows but for some it does.
If you are limited to 32 bit windows you can try reducing the genomic window size in which bams are loaded. Select "View > Preferences > Alignments" tab and reduce the "Visibility Window size", the default is 30, try 10.
The splicing track takes very little memory, it should in fact be off by default. You can set that in preferences also.
The visibility window reduction might be enough, but basically the computer is a bit underpowered for this application.
Jim
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