Partial Lastz Process Timeouts in make_lastz_chains

[ZhaoHang-bio]

Hi,

I've been utilizing the make_lastz_chains tool with the following command:

/public/home/zhaohang/soft/make_lastz_chains-2.0.7/make_chains.py target query ${refgenome_softmasked} ${quegenome_softmasked} --pd chain_out -f --chaining_memory 100 --cluster_executor slurm --cluster_queue smp01,amd,low --keep_temp
I'm encountering an issue where some of the lastz subprocesses are timing out and failing to complete.

Could this be due to the large size of the genome or the high proportion of repetitive sequences? What would be the recommended approach to mitigate this issue? Should I reduce the chunk size or extend the runtime of the subprocesses, and if so, could you provide guidance on how to adjust these parameters effectively?