Parallelization of samples for baseline

[bounlu]

I want to create a baseline from 58 normal samples. I specified them in the config file and it runs fine with msisensor-pro baseline command.

However, even though I specified the number of threads high enough (-b 64), it still goes sequentially through the samples one by one, chrom by chrom and region by region. Each sample takes about 1 hour to finish totaling to about 58 hours in my case. Is there a way to efficiently parallelize this?

I can use GNU parallel to run 58 samples simultaneously, but then how can I merge the results into 1 reference file?