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GRIDSS: the Genomic Rearrangement IDentification Software Suite
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Unable to run GRIDSS jar #652

Closed vialimju closed 10 months ago

vialimju commented 10 months ago

Hi,

I ran virusbreakend that I installed under gridss (mamba environment)

virusbreakend -r /mnt/storage/resources/references/hg38/hg38.fa -j ~/gridss-2.2.3-gridss-jar-with-dependencies.jar -o MNH053_CF_virusbreakend.vcf --db ~/virusbreakenddb_20210401 MNH053_CF/MNH053_CF.bam

but I got

Error: Could not find or load main class gridss.Echo Caused by: java.lang.ClassNotFoundException: gridss.Echo Wed Jan 10 17:54:19 GMT 2024: Unable to run GRIDSS jar. Java 1.8 or later is required. Wed Jan 10 17:54:19 GMT 2024: java version: openjdk version "21.0.1-internal" 2023-10-17 OpenJDK Runtime Environment (build 21.0.1-internal-adhoc.conda.src) OpenJDK 64-Bit Server VM (build 21.0.1-internal-adhoc.conda.src, mixed mode, sharing) Wed Jan 10 17:54:19 GMT 2024: Exit status 0 for exit $EX_CONFIG

and when I checked which java that I got, it says "/home/silvia/mambaforge/envs/gridss2/bin/java"

I thought when I installed gridss, all dependencies including openjdk were also installed. Am I missing something here?

Thanks!

d-cameron commented 10 months ago

gridss-2.2.3-gridss-jar-with-dependencies.jar

That version of GRIDSS is so old that it doesn't have the gridss.Echo command required by virusbreakend. Try GRIDSS version 2.13.2.

vialimju commented 10 months ago

Thank you, that works now!

HuangYihang1222 commented 6 months ago

I want to know how to install the latest version of gridss via conda? I can only install gridss-2.8.0-0 using conda