Process execution failed due to exceeding the allocated runtime limit I do get the following error

[TILccit]

Hello,

I am running nf-core/sarek on Ubuntu 22.04.3 LTS (GNU/Linux 5.15.153.1-microsoft-standard-WSL2 x86_64). I encountered the error: "Process exceeded running time limit (8h)." To address this, I tried using a custom.config file as discussed in #932. However, I am still encountering the same error.

Could you please provide further guidance on resolving this issue?

Command: nextflow -log /mnt/f/ARIA/sarek_output/log/M14TIL55.log
run nf-core/sarek -r 3.4.2 -profile docker --input M14TIL55_sarekinput.csv --genome GATK.GRCh38 --outdir /pt55/out/ --max_cpus 8 --tools mutect2,strelka,vep,snpeff,controlfreec,ascat --only_paired_variant_calling -c custom.config

Execution_report error: Workflow execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: null.

The full error message was:

Error executing process > 'NFCORE_SAREK:SAREK:FASTQC (55_healthy-1)'

Caused by: Process exceeded running time limit (8h)

Command executed:

printf "%s %s\n" noinfo-pt55healthy_R1_001.fastq.gz 55_healthy-1_1.gz noinfo-pt55healthy_R2_001.fastq.gz 55_healthy-1_2.gz | while read old_name new_name; do [ -f "${new_name}" ] || ln -s $old_name $new_name done

fastqc \ --quiet \ --threads 4 \ --memory 4096 \ 55_healthy-1_1.gz 55_healthy-1_2.gz

cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:FASTQC": fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS

Command exit status:

Command output: application/gzip application/gzip

Command wrapper: application/gzip application/gzip

Work dir: /mnt/f/ARIA/work/0b/66d2170cbbe48f92750fc33fc0ca1e

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

Please note that: My custom.config is params { max_memory = 128.GB max_time = 144.h } process {

 withName: 'NFCORE_SAREK:SAREK:FASTQC (55_healthy-1)' {
    time = 48.h // Specific time limit for this process

} } process {

 withName: 'NFCORE_SAREK:SAREK:FASTQC (55_baseline-1)' {
    time = 48.h // Specific time limit for this process

} } process {

 withName: 'NFCORE_SAREK:SAREK:FASTQC (55_progression-1)' {
    time = 48.h // Specific time limit for this process

} }

### .command.log from Work dir: /mnt/f/ARIA/work/0b/66d2170cbbe48f92750fc33fc0ca1e

application/gzip application/gzip Error response from daemon: cannot stop container: nxf-WF6UjjdSRFxhxbOdAIedosOd: tried to kill container, but did not receive an exit event

[TILccit]

FriederikeHanssen Could you please check this? Thanks in advance

[FriederikeHanssen]

Hi! You need to remove the task.id. Try this:

process {

     withName: 'NFCORE_SAREK:SAREK:FASTQC' {
        time = 48.h // Specific time limit for this process
     }
 }

[TILccit]

Thanks FriederikeHanssen, I will post with updates.