can't set java opts for rule recalibrate_base_qualities

[gernophil]

Hey everyone,

I'm trying to allocate some more memory to rule recalibrate_base_qualities since it's taking ages. I tried to allocate more memory and threads through the java opts, but the rule fails. I can't provide an error message. I'm running on a cluster and the log says I should look in the log files of the involved rules. This log file is empty though.

This is my code for the rule:

rule recalibrate_base_qualities:
    (unchanged)
    params:
        (unchanged)
        java_opts="-Xmx4G -XX:ParallelGCThreads=8", # also tried just: java_opts="-Xmx4G",
    threads: 8
    resources:
        mem_mb=32768,
        time="12:00:00", # just for cluster scheduling
    wrapper:
        "0.74.0/bio/gatk/baserecalibrator"

Can anyone help me spot the error?

Thanks in advance