I am looking for a FastQC alternative, we run FastQC on our cluster which doesn't work so well with java. By that I mean java is incapable of listening to slurm resource limits and tries to allocate way more memory than it actually needs. Since we have a heterogenous cluster this means that we have to set FastQC to request more than 32GB of ram per execution, which just wastes resources.
Why would java listen to slurm resource limits? Shouldn't you ask slurm to accommodate java by setting --mem instead?