quast time limit of 2 days

[ecologysarah]

Hi,

I'm trying to assemble a eukaryote genome, which takes time to run. However, the process keeps failing with the error

ERROR ~ Error executing process > 'ASSEMBLY_QC:quast (diplotaxis_tenuifolia:strategy_2)'

Caused by:
  Process exceeded running time limit (2d)

In the config file I have set the parameters:

 // starting values for the assembly jobs (and quast) to ask for in the very first try
  start_asm_mem              = 400.GB
  start_asm_cpus             = 100
  max_time                   = '120.h'

  // maximum values to be used on automatic second try in case of lack of memory (all jobs)
  max_memory                 = 500.GB
  max_cpus                   = 100
  max_time                   = '150.h'

I assume the 2-day limit must be hard-coded somewhere within the pipeline. Would you be able to advise how to modify it please?

[fmalmeida]

Hi there!

It used 2 days even in the second try?

I ask because max_time is only used on the second try.

Can you share the config you used completely, so I can check it?

I would say to overwrite the time in the first try you would need:

process {

withName:quast {
      time = '150.h'
}

}