Hi snandi,
Thank you for checking the system logs. Your job did indeed run out of memory. Did your job print out something that said “recovery mode”? That typically incurs a penalty for RAM. We will be making updates in our next release to reduce memory use and give users more control over peak memory use.
One thing you can try now is to pass --bwa-options="--reduce-batch-size" as that may help. Otherwise the other option would be to use a system with more RAM for this particular case.