PBSV system requirements

PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

BSD 3-Clause Clear License

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PBSV system requirements #697

Closed MKaandemir closed 1 month ago

MKaandemir commented 1 month ago

Hello, I'm interested in optimizing CPU usage for PBSV. What would you recommend for 30X WGS HiFi data in terms of RAM and CPU resources?

MKaandemir commented 1 month ago

I used 8 cpu and 48 gb ram for just chromosome 1 but it took like 4 hour. Is it normal?

armintoepfer commented 1 month ago

Sounds about right. Modern laptops already have 8 CPU cores. Please use a reasonable sized HPC node when processing a whole human genome.

MKaandemir commented 1 month ago

Could you define what constitutes a reasonably sized HPC node? Despite allocating extra CPUs, the processing time hasn't decreased. I plan to use this for numerous samples, so it needs to be optimized for cost and performance. It runs on AWS Batch, so I prefer not to use machines with more than 8 CPUs for this tool.