Open dudududu12138 opened 6 months ago
Hi, Sorry I didn't see this issue earlier. It shouldn't take 6 hours to run a 34G bam file. Could you check the class() of core as I think it might be being read in as a character and not an integer which might be interpreted as 1 core and not 20. Adding as.interger(core) should help I hope. Kind Regards, Andre Sim
Hi, I used bambu on one sample. The alignment result(.bam) of this sample is about 34G. And I run bambu on HPC cluster. I set the cpu number to 20. Then run it. But it took 6 hours to finish the job. And the cpu efficiency is only 5%. That is , only 1 cpu was used by bambu. I am so confused. Can you help me? Thanks! Below is my R code:
Below is my slurm code (submit my R script to the HPC cluster):