Please let me know if more info is needed to know better what's happening. Thank you in advance for any help

I see A LOT of processes given the initial number of FASTQ files. I'm concerned about your intervals file, you might want to play with the nucleotide_per_second parameter.

Thanks for your suggestion

How many columns does your intervals file have? If it is more than 3, maybe try with just the first 3. Sarek is designed to use the 5th column (score) for timing information, but if those numbers are anything else, it can start hundreds of thousand of processes and be horribly inefficient. 🤞

It has 3 columns

Could be that the file has too many intervals, then. When you find the proper BED file for your kit, you'll see how that behaves. 🤞