Snakemake error: "Removing output files of failed job since they might be corrupted:"

1

Hi!

I have a pipeline to process sequencing results, but the last rule gets an error:

Error in rule bwa_unmapped_hg38_samtools3:
    jobid: 8
    output: out/id_SRR13510812_unmapped_hg_2.txt
    shell:
        diff out/id_SRR13510812_2.txt out/id.SRR13510812.txt > out/id_SRR13510812_unmapped_hg_2.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job bwa_unmapped_hg38_samtools3 since they might be corrupted:
out/id_SRR13510812_unmapped_hg_2.txt
[Thu Jun 24 14:18:52 2021]
Error in rule bwa_unmapped_hg38_samtools3:
    jobid: 7
    output: out/id_SRR13510812_unmapped_hg_1.txt
    shell:
        diff out/id_SRR13510812_1.txt out/id.SRR13510812.txt > out/id_SRR13510812_unmapped_hg_1.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job bwa_unmapped_hg38_samtools3 since they might be corrupted:
out/id_SRR13510812_unmapped_hg_1.txt
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

The last rule looks like this. I am using the diff line command to compare two samples:

rule bwa_unmapped_hg38_samtools3:
        input: data1=config["out"] +"id_{sample}_{read}.txt" , data2=config["out"] + "id.{sample}.txt"
        output: config["out"]+ "id_{sample}_unmapped_hg_{read}.txt"
        shell: "diff {input.data1} {input.data2} > {output}"


Snakemake

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