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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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bamQC runtime exceeded [BUG] #425

Closed giesselmann closed 3 years ago

giesselmann commented 3 years ago

Hi there!

I have a problem running the sarek pipeline, the bamQC jobs get canceled after a day and I'm failing to increase the runtime either via command line or config file.

Check Documentation

I have checked the following places for your error:

Description of the bug

I'm running the pipeline with either

--max_time '4.day'

or a config file:

process { withLabel: 'BamQC' { time = '96h' }}

Ressources of the machine seem to be correctly determined:

Max Resources : 128 GB memory, 16 cpus, 10d time per job

And bamQC is almost making it, before getting cancled after 1d of runtime (last line from job output):

Processed 450 out of 485 windows...

Steps to reproduce

Steps to reproduce the behaviour:

  1. Command line:

    nextflow run nf-core/sarek -profile conda -c params.config --input input.tsv --genome GRCh37 --resume

  2. See error: See also nextflow.log (line 4135)

'BamQC (HCT116-HCT116_1_1)' Caused by: Process exceeded running time limit (1d) Command executed: qualimap --java-mem-size=128G bamqc -bam HCT116_1_1.bam --paint-chromosome-limits --genome-gc-distr HUMAN -nt 16 -skip-duplicated --skip-dup-mode 0 -outdir HCT116_1_1 -outformat HTML

Expected behaviour

I assumed either command line or config file should be able to change the bamQC runtime.

Log files

Have you provided the following extra information/files:

System

Nextflow Installation

Container engine

Additional context

giesselmann commented 3 years ago

Hi, can anyone help? We're still stuck in processing our samples due to the runtime limit. Pay

FriederikeHanssen commented 3 years ago

Hi @giesselmann! Sorry didn't see this before. Could you post your complete config file?

giesselmann commented 3 years ago

Hi, it's online the posted line: process { withLabel: 'BamQC' { time = '96h' }} We're currently trying the same with 'withName'. I'm not familiar with nextflow at all, sorry. Thanks for help, Pay

FriederikeHanssen commented 3 years ago

ah yes, it should work with:

process{
      withName:'BamQC'{
            time = '96.h'
     }
}

--max_time --max-cpus etc. only sets a maximum to prevent nextflow to request more than for example available on your cluster, but does not increase the resources for an individual process. There is a bit of documentation here https://nf-co.re/usage/configuration?q=--max_cpus#max-resources

giesselmann commented 3 years ago

It does, thanks for the support!