-
Notifications
You must be signed in to change notification settings - Fork 384
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Error while querying reads in gnome terminal #1561
Comments
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? |
Hello, Here is the log file: igv_error.log |
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. |
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)
|
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.
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:
': https://data.broadinstitute.org/igv/projects/downloads/2.18/IGV_2.18.2.zip
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)
The text was updated successfully, but these errors were encountered: