Bam file not loading

[Daniel Faulkner]

Hi,

I am currently having an issue where bam files are not loading on a few PCs but no error is produced. These particular bam files will load on other PCs with the same setup seemingly without issue. 

Currently on Windows 10 using IGV 2.11.9, one user had these issues with 2.11.7 as well.

I have tried renaming the preference file etc but are there other causes for this issue that I may be able to perform? 

The logs do not seem to provide any insight for this issue so I appreciate it may not be something that is easily solvable with the little information I have provided.

Thanks,

[igv-help]

Hi,

I'm not sure we'll be able to help with this but can you define what you mean by. "not loading"?  Does IGV hang?  Are you loading by URL,  local file, by port command or http link, or some other way?  If you could provide a screenshot of what you see after attempting a load that might help.

[Daniel Faulkner]

Hi,

I wasn't sure if you would be able to but thought it worth a shot as we don't appear to have many other options now.

IGV doesn't hang, when the file is selected it appears to load but just displays as below;

And from the log files;

INFO [Feb 04,2022 09:29] [Main] Startup  IGV Version 2.11.9 12/21/2021 12:15 AM
INFO [Feb 04,2022 09:29] [Main] Java 11.0.13 (build 11.0.13+8) 2021-10-19
INFO [Feb 04,2022 09:29] [Main] Java Vendor: Eclipse Adoptium https://adoptium.net/
INFO [Feb 04,2022 09:29] [Main] JVM: OpenJDK 64-Bit Server VM Temurin-11.0.13+8  
INFO [Feb 04,2022 09:29] [Main] OS: Windows 10 10.0 amd64
INFO [Feb 04,2022 09:29] [Main] IGV Directory: C:\Users\kevinbaker1\igv
INFO [Feb 04,2022 09:29] [GenomeManager] Loading genome: C:\Users\kevinbaker1\igv\genomes\hg19.genome
INFO [Feb 04,2022 09:29] [GenomeManager] Loading genome: C:\Users\kevinbaker1\igv\genomes\hg19.genome
SEVERE [Feb 04,2022 09:29] [IGVPreferences] No default value for: CIRC_VIEW_ENABLED
INFO [Feb 04,2022 09:30] [IGV] Loading 1 resources.
INFO [Feb 04,2022 09:30] [IGV] Loading 1 resources.
INFO [Feb 04,2022 09:30] [TrackLoader] Loading resource, path W:\Share\BAM-FILE-STORE\Myeloid\220126*****\******.bam

It is a local file albeit on a mapped drive, it only happens to specific people, there don't appear to be issues with the files as these load for other users. As far as I am aware there should be no differences in setup or settings between PCs either.

Many thanks,

Daniel

[James Robinson]

That looks perfectly normal if there are no alignments at that location.    Are you certain that there are? 

It might be interesting to copy the file to be truly local and test, to eliminate any weird problem with the mapped drive.

Another data point, although I'm not sure what it will tell us, would be to see if the file can be loaded from igv-webapp (https://igv.org/app).   The web app is 100% client, it runs in your browser, nothing is uploaded and you use it in basically the same way.   Load the bam from "Tracks > Local File...".   

Again, to emphasize, be sure you test a genome location where you know there are alignments.

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[Daniel Faulkner]

Thanks for looking, there definitely should be alignments in that position, it works on another PC but I will make sure that we try copying the file to the C drive and see if the Web app has been tried. 

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