IGV Unable to Open files on a Mac M3

[Russell Bainer]

Hi everyone, I'm running into an issue in which IGV version 2.17.1 (MacOS app with Java included) is unable to launch the popup window to load files.

IGV is able to load as usual, but when I select `Load from File...` from the menu the application beachballs and then stops without producing an error. 

I've looked around for other similar issues but haven't seen anything described. Does anyone have any ideas about how to troubleshoot this? 

[Arghavan Ashouri]

Hi, 
I had the same issue, but with an older version of IGV. I downloaded the newest version (2.17.2) and now it works. 

Hope this helps, 
Ari 

[igv-help]

Its difficult to say without more information.  I would suggest you try installing Java independently, and then use the app without Java included.    If you do not have Java release 17 or greater installed already you can download an open source version from here:  https://adoptium.net/

[Russell Bainer]

Thanks a lot folks. Reinstalling Java with a fresh download worked for me!

[Eduardo Groisman]

Hi, everyone, I have installed igv_2.18.2 2 with and without Java versions.  The DNA sequence for the genome of interest opens but I cannot load my RNA-seq and ChIP-seq files.  Do you have any suggestions?  Thanks a lot.

[James Robinson]

There's not enough information here to help you.  What exactly are you doing, and what is going wrong?  Screenshots might help.

[Eduardo Groisman]

Hello, James,

I downloaded IGV MacOS App with Java included (igv_2.18.2 2) to my new MacBook Pro with M3 chip. I can open the program and my genome of interest loads perfectly well.  However, when I go to "File", "Load from file" to visualize RNA-seq and ChIP-seq data, I get error messages (screen shots attached).  The RNA-seq and ChIP-seq files are the same I could visualize with a previous version of IGV on my Intel-based MacBook Pro.

When I downloaded "IGV MacOS App Separate Jave 17 required" and Java, IGV would not open.

Thanks for your help.

Eduardo

[James Robinson]

OK, the first problem is caused by a mismatch between the sequence names in your fasta file and the names in your data files.  The error message indicates that your data file has a sequence name that starts with "CP...",  the sequence name in the fasta (genome) file starts with "gi|..."

I can't guess on the second problem without more information, what version of Java did you install?  In any event the no-Java version will behave exactly like the Java version.

I do not know why your "previous version? of IGV could resolve this sequence name mismatch, but if you tell me which version exactly I can investigate.  

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[Eduardo Groisman]

Thank you, James.  

Are you suggesting to load the genome as a FASTA file?

I installed version 17 of Java.

The previous version of IGV I was using in my previous (Intel chip-based) computer is IGV_2.4.16.

[James Robinson]

Hi,

I am simply pointing out that your BAM file uses a sequence name of CP001363.1.   The reference sequence on the other hand has a sequence name of gi|378448274|ref|NC_016856.1.   Obviously these do not match.   IGV can detect the alias NC_016856.1 <-> gi|378448274|ref|NC_016856.1,   but there are no sequence names in this reference with the name CP001363.1. 

If you have the fasta this BAM was aligned to then yes,  using it as the reference (i.e. load it from the Genome menu) will fix the issue.   

I will look at the older version and see if I can determine how it resolved this.

[James Robinson]

I'm not able to run 2.4.16 on my current system, however I have added an alias for CP001363.1 <-> gi|378448274|ref|NC_016856.1.   If you refresh your genome this should be fixed.   To do this just select it again from the "Genomes > Load from Server.." menu. 

[Eduardo Groisman]

Thank you.  I will try this later.