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MPUSP / nf-core-crispriscreen

Process next generation sequencing data obtained from CRISPRi repression library screenings
MIT License
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Pipeline requires at least 10 CPUs #10

Closed ute-hoffmann closed 1 year ago

ute-hoffmann commented 1 year ago

Pipeline does currently not run on machines with less than 10 CPUs, since bowtie2-build and bowtie2 align seem to be configured in a way that they need at least 10 CPUs. (Error cause: Process requirement exceeds available CPUs -- req: 10; avail: 8)

ute-hoffmann commented 1 year ago

Detailed output regarding error:

Error executing process > 'NFCORE_CRISPRISCREEN:CRISPRISCREEN:BOWTIE2_BUILD (library.fasta)'

Caused by: Process requirement exceeds available CPUs -- req: 10; avail: 8

Command executed:

mkdir bowtie2 bowtie2-build --threads 10 library.fasta bowtie2/library cat <<-END_VERSIONS > versions.yml "NFCORE_CRISPRISCREEN:CRISPRISCREEN:BOWTIE2_BUILD": bowtie2: $(echo $(bowtie2 --version 2>&1) | sed 's/^.bowtie2-align-s version //; s/ .$//') END_VERSIONS

Command exit status:

Command output: (empty)

m-jahn commented 1 year ago

The resources of the current machine can be allocated in the nextflow.config file, this one: https://github.com/m-jahn/nf-core-crispriscreen/blob/master/nextflow.config

On line 81:

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = '20.GB'
    max_cpus                   = 10
    max_time                   = '1.h'
m-jahn commented 1 year ago

Issue seems resolved.