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phac-nml / mpox-nf

A monkeypox virus (MPXV) assembly pipeline using Nextflow for host-removal, reference-based assembly, and generation of sequence quality metrics for Illumina paired-end data using a shotgun metagenomic sequencing approach.
Apache License 2.0
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availMemory error in HPC #7

Closed abulenciamiguel closed 2 years ago

abulenciamiguel commented 2 years ago

Tried running it in HPC and got this error below but it ran fine with done in local desktop.

Local avail `memory` attribute cannot zero. Expression: (availMemory > 0). Values: availMemory = 0

 -- Check script '/data/apps/monkeypox-nf/./workflows/mpx_main.nf' at line: 30 or see '.nextflow.log' file for more details
DarianHole commented 2 years ago

Hi @ufuomababatunde,

Thanks for the issue report! What executor are you using for your HPC environment? It likely has to do with that not being set correctly and you may need to generate your own config file or I can look to add one in for you.

abulenciamiguel commented 2 years ago

Hello @DarianHole ,

Thank you for the idea. I added the lines below in the nextflow.config and it worked.

executor {
  name = 'local'
  cpus = 35
  memory = '150 GB'
}