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您好我正在尝试使用snakemake 运行管道。具体来说，我按照此处指定的说明运行演示 rna-seq 分析管道：https ://gagneurlab-drop.readthedocs.io/en/latest/installation.html

当我运行时，snakemake --cores 1我收到以下错误消息::

    Error in rule aberrantExpression_bamStats:
    jobid: 26
    output: /Users/00104561/drop_demo/Output/processed_data/aberrant_expression/v29/coverage/HG00126.1.M_111124_8.tsv
    shell:
        
        # identify chromosome format
        if samtools idxstats /Users/00104561/drop_demo/Data/rna_bam/HG00126.1.M_111124_8_chr21.bam | grep -qP "^chr";
        then
            chrNames=$(cut -f1 Scripts/AberrantExpression/pipeline/resource/chr_UCSC_NCBI.txt | tr '
' '|')
        else
            chrNames=$(cut -f2 Scripts/AberrantExpression/pipeline/resource/chr_UCSC_NCBI.txt | tr '
' '|')
        fi

        # write coverage from idxstats into file
        count=$(samtools idxstats /Users/00104561/drop_demo/Data/rna_bam/HG00126.1.M_111124_8_chr21.bam | grep -E "^($chrNames)" |                 cut -f3 | paste -sd+ - | bc)

        echo -e "HG00126.1.M_111124_8   ${count}" > /Users/00104561/drop_demo/Output/processed_data/aberrant_expression/v29/coverage/HG00126.1.M_111124_8.tsv
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

任何帮助，将不胜感激！我对生物信息学很陌生！

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1 回答 1

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消息“其中一个以非零退出代码退出的命令”表示 shell 命令已成功启动，但它报告了错误（非零退出代码）。

所以你让snakemake运行的命令出了点问题。尝试直接从命令行运行报告的命令而不使用snakemake，这样调试可能更容易。

最近对类似问题的回答很好地解释了这一点：https ://stackoverflow.com/a/67176454/663466

于 2021-04-21T14:31:30.873 回答