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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
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Error while querying reads in gnome terminal #1561

Open aamahale opened 1 month ago

aamahale commented 1 month ago

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=${igvdir} -- ./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

  1. 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)

image

jrobinso commented 1 month ago

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 commented 1 month ago

Hello,

Here is the log file: igv_error.log

jrobinso commented 1 month ago

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 igv-team@broadinstitute.org and either attach it there or I can respond with a private dropbox link.

aamahale commented 1 month ago

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)