Cannot load merged BAM list files, or single BAMs for full utility

[Spencer Tye]

I'm on Windows. I'd attach the log file, but cant seem to see how to even attach a file to these messages, unless it's a photo.

I believe the issue centers around the type of index file. I have a 'filename.BAM.bai' format. But I've changed it to just 'filename.bai' and this does not resolve the issue. However I created the index files exactly how IGV has said they need to be made, so either way, the issue shouldn't be occuring.

The list I'm importing to IGV contains the following:

S:/Computation/R/MixOmics Workplace/BAMS/bam01.bam
S:/Computation/R/MixOmics Workplace/BAMS/bam02.bam
S:/Computation/R/MixOmics Workplace/BAMS/bam03.bam
S:/Computation/R/MixOmics Workplace/BAMS/bam04.bam
S:/Computation/R/MixOmics Workplace/BAMS/bam05.bam

And the name of an index file for one of these would then be:

S:/Computation/R/MixOmics Workplace/BAMS/bam01.BAM.bai

They are all in the same folder with the BAM files, so there souldn't be an access to the files issue like it's stating there is but here is the error I receive:

Unexpected error: An error occurred while accessing: S:\Computation\R\MixOmics Workplace\BAMS\bam01.bam
Error loading BAM file: org.broad.igv.exceptions.DataLoadException: An error occurred while accessing: S:\Computation\R\MixOmics Workplace\BAMS\bam01.bam.bai
Index file not found. Tried
S:\Computation\R\MixOmics Workplace\BAMS\bam01.bai
S:\Computation\R\MixOmics Workplace\BAMS\bam01.bam.csi
S:\Computation\R\MixOmics Workplace\BAMS\bam01.csi.
See igv.log for more details

As I've said, I have renamed the index files to just 'filename.bai' but the error message it give me is still exactly the same, implying that it is looking for an index file with the exact same name of the index file in the location it is looking for it in, yet somehow cannot see the file.

[Spencer Tye]

The versio of IGV I'm using is 2.16.1

Here's the contents of the igv0.log

SEVERE [Jul 16,2024 13:58] [TrackLoader] An error occurred while accessing:    S:\Computation\R\MixOmics Workplace\BAMS\bam01.bam<br>Error loading BAM file: org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    S:\Computation\R\MixOmics Workplace\BAMS\bam01.bam.bai<br>Index file not found.  Tried <br>S:\Computation\R\MixOmics Workplace\BAMS\bam01.bai<br>S:\Computation\R\MixOmics Workplace\BAMS\bam01.bam.csi<br>S:\Computation\R\MixOmics Workplace\BAMS\bam01.csi
SEVERE [Jul 16,2024 13:58] [TrackLoader] org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    S:\Computation\R\MixOmics Workplace\BAMS\bam01.bam<br>Error loading BAM file: org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    S:\Computation\R\MixOmics Workplace\BAMS\bam01.bam.bai<br>Index file not found.  Tried <br>S:\Computation\R\MixOmics Workplace\BAMS\bam01.bai<br>S:\Computation\R\MixOmics Workplace\BAMS\bam01.bam.csi<br>S:\Computation\R\MixOmics Workplace\BAMS\bam01.csi
at org.igv/org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:88)
at org.igv/org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:53)
at org.igv/org.broad.igv.sam.reader.AlignmentReaderFactory.getBamListReader(AlignmentReaderFactory.java:125)
at org.igv/org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:91)
at org.igv/org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:57)
at org.igv/org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:78)
at org.igv/org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:910)
at org.igv/org.broad.igv.track.TrackLoader.load(TrackLoader.java:161)
at org.igv/org.broad.igv.ui.IGV.load(IGV.java:1249)
at org.igv/org.broad.igv.ui.IGV.lambda$load$5(IGV.java:1281)
at org.igv/org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)

SEVERE [Jul 16,2024 13:58] [LongRunningTask] Exception running task
SEVERE [Jul 16,2024 13:58] [LongRunningTask] org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    S:\Computation\R\MixOmics Workplace\BAMS\bam01.bam<br>Error loading BAM file: org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    S:\Computation\R\MixOmics Workplace\BAMS\bam01.bam.bai<br>Index file not found.  Tried <br>S:\Computation\R\MixOmics Workplace\BAMS\bam01.bai<br>S:\Computation\R\MixOmics Workplace\BAMS\bam01.bam.csi<br>S:\Computation\R\MixOmics Workplace\BAMS\bam01.csi
at org.igv/org.broad.igv.track.TrackLoader.load(TrackLoader.java:272)
at org.igv/org.broad.igv.ui.IGV.load(IGV.java:1249)
at org.igv/org.broad.igv.ui.IGV.lambda$load$5(IGV.java:1281)
at org.igv/org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)

INFO [Jul 16,2024 14:19] [Main] Startup  IGV Version 2.16.1 04/19/2023 02:19 AM
INFO [Jul 16,2024 14:19] [Main] Java 11.0.13 (build 11.0.13+8) 2021-10-19
INFO [Jul 16,2024 14:19] [Main] Java Vendor: Eclipse Adoptium https://adoptium.net/
INFO [Jul 16,2024 14:19] [Main] JVM: OpenJDK 64-Bit Server VM Temurin-11.0.13+8  
INFO [Jul 16,2024 14:19] [Main] OS: Windows 10 10.0 amd64
INFO [Jul 16,2024 14:19] [Main] IGV Directory: C:\Users\tyesp\igv
INFO [Jul 16,2024 14:19] [Main] Resoluction scale = 2.0
INFO [Jul 16,2024 14:19] [CommandListener] Listening on port 60151
INFO [Jul 16,2024 14:19] [GenomeManager] Loading genome: C:\Users\tyesp\igv\genomes\mm39.json
SEVERE [Jul 16,2024 14:19] [ReferenceFrame] Null chromosome:
INFO [Jul 16,2024 14:19] [TrackLoader] Loading resource:  https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/ncbiRefSeq.txt.gz