snakemake errors and threads

Question

[Assa Yeroslaviz]

I'm trying to implement a snakemake workflow for my fastq files

This is my rule for mapping: gz_command="--readFilesCommand zcat" if config["gzipped"] else ""

main snakefile

configfile:"config.yaml"

SAMPLES=["1_S1", "2_S2", "3_S3", "4_S4"]

rule all:
   input:
      directory("data/starIndex/"),
      bam=expand("mapped/star/bamFiles/{sample}.bam", sample=SAMPLES),
      counts=expand("mapped/star/CountsFiles/{sample}.counts.tab", sample=SAMPLES),
      expand("mapped/star/bamFiles/{sample}.bam.bai", sample=SAMPLES)

# Genome indexing
include:"./Star.GenomeIndexing.Snakefile"

# Genome Mapping
include:"./Star.Mapping.Snakefile"

Mapping step (Star.Mapping.Snakefile)

rule map_star:
    input:
        R1='data/samples/paired-end/{sample}_R1.fastq',
        R2='data/samples/paired-end/{sample}_R2.fastq',
        index=directory("data/starIndex/")
    output:
        bam='mapped/star/bamFiles/{sample}.bam',
        counts='mapped/star/CountsFiles/{sample}.counts.tab'
    params:
        prefix = 'mapped/bams/star/{sample}.',
        starlogs = 'mapped/starlogs',
        gz_support=gz_command
    threads: 16
    shell:
        r'''
        STAR --runThreadN {threads}\
             --genomeDir {input.index}\
             --outFileNamePrefix {params.prefix} --readFilesIn {input.R1} {input.R2} {params.gz_support}\
             --outSAMtype BAM SortedByCoordinate\
             --limitBAMsortRAM 50000000000\ #50 Gib
             --quantMode GeneCounts\
             --outReadsUnmapped Fastx &&\
             mv {params.prefix}Aligned.sortedByCoord.out.bam {output.bam} &&\
             mv {params.prefix}counts.tab {output.counts} &&\
             mkdir -p {params.starlogs} &&\
             mv {params.prefix}Log.final.out {params.prefix}Log.out {params.prefix}Log.progress.out {params.starlogs}
        '''

rule index:
    input:
        'mapped/star/bamFiles/{sample}.bam'
    output:
        'mapped/star/bamFiles/{sample}.bam.bai'
    shell:
        'samtools index {input}'

I have the problem that the threads parameter is not being recognized When I testing the --dryrun I see this command for the mapping:

STAR --runThreadN 1\
     --genomeDir data/starIndex/\
     --outFileNamePrefix mapped/bams/star/1_S1. --readFilesIn data/samples/paired-end/1_S1_R1.fastq data/samples/paired-end/1_S1_R2.fastq \
     --outSAMtype BAM SortedByCoordinate\
     --limitBAMsortRAM 50000000000\ #50 Gib
     --quantMode GeneCounts\
     --outReadsUnmapped Fastx &&\
 ...

which tells me that there is only one thread active. Why is that?

How can I fix this to the parameter set in the command itself?

thanks Assa

Answer 1

[Sej Modha]

Can you post the command you used to run that snakemake file? Did you provide -j parameter to >1 in order for snakemake to use multiple threads?

[Assa Yeroslaviz]

thanks. i forgot to add it.

[Sej Modha]

Please do not close a post after it has received a response. If a given answer resolves the question then please accept it so others can get an indication on how to resolve this.