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"
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:
Can anyone help me spot the error?
Thanks in advance