Increase the delay between ASCAT jobs
When submitting multiple jobs to the cluster there is a default delay of 30 seconds that is added to each job. The delay is there because most jobs start by copying data from the network to the local node and this will perform better if not all jobs start at the same time.
The BAM files for WGS data that ASCAT uses is however very large and they take several minutes to copy. The result is that too many jobs are copying data from the same server at the same time and will take several hours just for the copy operation.
Slurm can probably be configured to take care of this (via partions, QoS, etc.) but since that is not in place, it may help a bit to increase the delay between ASCAT jobs to ~5 minutes.