Question

在染色体分散到checkpoint的步骤中，我需要在Snakemake中制作一个call copy number variants with GATK：

rule all:
    input:
        'aggregated/chr1'

# step that gives non-zero exit code error
checkpoint scattering:
    input:
        interval = 'gcfiltered_{chr}.interval_list'
    output:
        directory('scatter_{chr}')
    shell:
        'mkdir -p {output} && '
        'gatk --java-options "-Xmx8G" IntervalListTools '
        '--INPUT {input.interval} '
        '--SUBDIVISION_MODE INTERVAL_COUNT '
        '--SCATTER_CONTENT 600 '
        '--OUTPUT {output}'

def aggregate_scatter(wildcards):
    checkpoint_output = checkpoints.scattering.get(**wildcards).output[0]
    return expand('scatter_{chr}/{i}/scattered.interval_list',
            chr=wildcards.chr,
            i=glob_wildcards(os.path.join(checkoint_output, '{i}/scattered.interval_list')).i)

# dummy rule to check if scattered files will be aggregated:
rule aggregate:
    input:
        aggregate_scatter
    output:
        "aggregated/{chr}"
    shell:
        "cat {input} > {output}"

但是scattering规则失败。尽管输出正确产生，但它会给出错误(exited with non-zero exit code)并删除输出。我尝试添加|| true，但没有用。

但是，当我在snakemake之外运行命令时，它的退出状态为0时运行良好：

mkdir -p scatter_chr1 && gatk --java-options "-Xmx8G" IntervalListTools --INPUT gcfiltered_chr1.interval_list --SUBDIVISION_MODE INTERVAL_COUNT --SCATTER_CONTENT 600 --OUTPUT scatter_chr1
echo $?

我使用Snakemake 5.5.4和GATK 4.1.2.0。输入文件示例（gcfiltered_chr1.interval_list）：

@HD VN:1.6
@SQ SN:chr1 LN:122678785    UR:file:canFam3.fa  M5:e4671b339daa96b7f11eb0b68fd999d8
chr1    100000  100999  +   .
chr1    101000  101999  +   .
chr1    102000  102999  +   .
chr1    103000  103999  +   .
chr1    104000  104999  +   .
chr1    105000  105999  +   .
chr1    106000  106999  +   .
chr1    107000  107999  +   .
chr1    108000  108999  +   .
chr1    109000  109999  +   .
chr1    110000  110999  +   .
chr1    111000  111999  +   .
chr1    112000  112999  +   .
chr1    113000  113999  +   .
chr1    114000  114999  +   .
chr1    115000  115999  +   .
chr1    116000  116999  +   .
chr1    117000  117999  +   .
chr1    118000  118999  +   .
chr1    119000  119999  +   .
chr1    120000  120999  +   .

Snakemake检查点（退出代码为非零）

0 个答案: