[Critical Bug] Sashimi Plot Popup Renders Blank Tracks on Windows 10 (IGV 2.17.4)

[lu yiming]

I am writing to report a persistent issue with the Sashimi Plot functionality in IGV 2.17.4.

The Problem Description: When I right-click a transcript and select "Sashimi Plot," the new visualization window opens but fails to render the coverage tracks and junction arcs. Only the gene/transcript annotation track at the bottom is visible; the data visualization area above it remains completely blank/white. This occurs for all transcripts I attempt to plot.

Environment and Configuration:

• IGV Version: 2.17.4 (Portable/ZIP distribution)

• OS: Windows 10

• Java Version: 17.0.10 (System default, as bundled JDK was not found/used)

• System RAM: 32 GB

• Data Files: BAM and GTF files are successfully loaded and displayed in the main IGV window. File paths have been restricted to use only ASCII characters (no Chinese or special characters) to rule out encoding issues.

Exhaustive Troubleshooting Steps Taken (Failure to Resolve):

To rule out memory, compatibility, and rendering issues, I have attempted the following steps without success:

1. Increased Memory Allocation: Set the -Xmx parameter in igv.bat to 8g.

2. Windows DPI Scaling Fix: Applied the "Override high DPI scaling behavior" (set to "System") compatibility setting to the system's core java.exe file, addressing common Java Swing rendering issues on high-resolution Windows screens.

3. Forced Software Rendering: Explicitly edited the igv.bat file to add the Java 2D parameter -Dsun.java2d.d3d=false to the startup command, disabling hardware acceleration to resolve potential graphics driver conflicts.

4. Log Analysis: The console output confirms no fatal Java Exceptions (such as OOM or Null Pointer) are thrown when the blank Sashimi window is launched, indicating a rendering logic failure rather than a thread crash.

Console Log Snippet: (A full log file is attached/provided below)

WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
java version "17.0.10" 2024-01-16 LTS
Java(TM) SE Runtime Environment (build 17.0.10+11-LTS-240)
Java HotSpot(TM) 64-Bit Server VM (build 17.0.10+11-LTS-240, mixed mode, sharing)
INFO [12月 17,2025 11:15] [Main] Startup  IGV Version 2.17.4 03/26/2024 12:38 PM
INFO [12月 17,2025 11:15] [Main] Java 17.0.10 (build 17.0.10+11-LTS-240) 2024-01-16
INFO [12月 17,2025 11:15] [Main] Java Vendor: Oracle Corporation https://java.oracle.com/
INFO [12月 17,2025 11:15] [Main] JVM: Java HotSpot(TM) 64-Bit Server VM
INFO [12月 17,2025 11:15] [Main] OS: Windows 10 10.0 amd64
INFO [12月 17,2025 11:15] [Main] IGV Directory: C:\Users\lenovo\igv
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
INFO [12月 17,2025 11:15] [CommandListener] Listening on port 60151
INFO [12月 17,2025 11:15] [GenomeManager] Loading genome: D:\项目\西瓜多组学\S116.fasta
WARNING [12月 17,2025 11:15] [LoadFromServerAction] No data found for current genome.
INFO [12月 17,2025 11:15] [TrackLoader] Loading resource:  D:\项目\西瓜多组学\transcriptome\StringTie\S116\2_merged_gtf\merged_S116.gtf
INFO [12月 17,2025 11:15] [TrackLoader] Loading resource:  F:\项目\S116_T2.sorted.bam

Given that all standard workarounds have failed, I believe this may be a bug within the Sashimi Plot's drawing component when running on this specific Windows/Java 17 environment.

Could you please confirm if this is a known rendering bug in version 2.17.4, or suggest any alternative older versions that are less prone to such graphics issues?

Thank you for your assistance.

Best regards

[lu yiming]

[igv-help]

I thinkthis has been fixed in the latest release (2.19.7).   Is there a reason you need to use an older version?

[lu yiming]

Thank you for reply and for giving the useful suggestion. I download the latest release (2.19.7) and the problem has been solved.

Yiming