Error while querying reads in gnome terminal

[aamahale]

Description:
We are trying to visualize the reads from SARS CoV2 samples on the gnome terminal. Upon uploading the sample file we see the following error.

Error encountered querying alignments: java.lang.RuntimeException: java.io.EOFException

Current version: IGV_Linux_2.18.2

Command for execution:
gnome-terminal --working-directory=${igv_dir} -- ./igv.sh

Sample input: SRRxxx.bam
Reference genome: Sars-CoV-2

Approaches to troubleshoot:

1. Updated IGV version

Command line IGV and igvtools for all platforms

': https://data.broadinstitute.org/igv/projects/downloads/2.18/IGV_2.18.2.zip

2. Updated the java version:
   openjdk version "17.0.12" 2024-07-16
   OpenJDK Runtime Environment (build 17.0.12+7-Ubuntu-1ubuntu220.04)
   OpenJDK 64-Bit Server VM (build 17.0.12+7-Ubuntu-1ubuntu220.04, mixed mode, sharing)

[jrobinso]

Hi, there's not enough information here to do a diagnosis. Could you post the contents of your igv log file, which should be in /igv/igv0.log?

[aamahale]

Hello,

Here is the log file: igv_error.log

[jrobinso]

I suspect this has something to do with SARS being such a small sequence, and we are hitting some edge case. Are you able to share the bam file? If so send an email to [email protected] and either attach it there or I can respond with a private dropbox link.

[aamahale]

Thank you for looking into this issue. We were able to run the tool fine by adding a different SARS CoV 2 reference (MN908947.3)