Error with running star via snakemake on cluster

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5.3 years ago

lawrence.hsu ▴ 10

I've posted on the author's issue page but I wanted to see if anyone else has encountered this problem. The pipeline runs fine locally but as soon as I push it to the cluster an error saying 'sbatch: error: Unable to open RNA Seq file'. I've also attached an image of the error.

rule STAR04:
    input:
        "02-trimmed/{sample}_trimmed.fq"
    output:
        sam="04-aligned-2pass/{sample}_ID/Aligned.out.sam",
        sum="04-aligned-2pass/{sample}_ID/Log.final.out"
    log:
       "logs/star/{sample}.log"
    shell:
        "/data/p_magnuson_lab/bin/STAR-2.6.0c/bin/Linux_x86_64/STAR "
        "--genomeDir /data/p_magnuson_lab/reference/mouse/STAR_index "
        "--runThreadN 8 "
        "--readFilesCommand zcat "
        "--twopassMode Basic "
        "--alignEndsType EndToEnd "
        "--alignIntronMax 1 "
        "--readFilesIn {input} "
        "--outFileNamePrefix 04-aligned-2pass/{wildcards.sample}_ID/ "
    " &> {log}"

enter image description here

snakemake software error • 1.4k views

ADD COMMENT • link 5.3 years ago by lawrence.hsu ▴ 10

1

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It looks like your cluster command is wrong.

ADD REPLY • link 5.3 years ago by Devon Ryan 105k

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I've posted on the author's issue page

Please include a link then.

ADD REPLY • link 5.3 years ago by WouterDeCoster 47k

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