how t speed running the run-asm-pipeline.sh

[Ao Qo]

Hello,everyone
I am running the run-asm-pipeline.sh. My command is : /data/01/user157/software/3d-dna/run-asm-pipeline.sh -r 1 M.aspalax.6.bp.p_ctg.fasta merged_nodups.txt. The M.aspalax.6.bp.p_ctg.fasta is from Hifiasm assembly and the merged_nodups.txt is from juicer pipline. I do not find the thread option in the run-asm-pipeline.sh, so I only set 1 CPU and 250G memory when I submit the task by SLURM. My data size is much lager : the merged_nodups.txt is 327G and the M.aspalax.6.bp.p_ctg.fasta is 2.9G. It has run for six days. But when I check the log file, it is running the step of iterating scaffolding for round 0. Is it correct? And any idea to save the time? Maybe should I increase the CPU setting?
Could you give me any suggestions?
Best wishes!
3ddna.log

[Olga Dudchenko]

Hello,

3d-dna is parallelized and will use all CPUs provided. The parallelization requires GNU parallel to be available in the path.

Best,

Olga

[Ao Qo]

Hello,

Maybe I misunderstood. Before I do not find the CPU parameter, so I set the  only 1 CPU. I will increase the CPU and then run. 

Thanks!