Question

我当前正在运行一个snakemake检查点，即使正确完成命令后，该检查点似乎仍在抛出非零退出代码，并且不确定如何解决该问题。

以下脚本的目的是解析坐标文件bed_file，从bam文件rna_file中提取所有区域，并最终组合这些区域。下面的代码，我的snakemake版本是5.6.0。

#Pull coordinates from a BAM file, and use the command samtools view to extract the corresponding #data, naming the output as the coordinate file, here named "6:25274434-25278245.bam". There are #an unknown number of output files

checkpoint pull_reads_for_BAM:
    input:
    ¦   bed_file = get_lncRNA_file,
    ¦   rna_file = get_RNA_file
    conda:
    ¦   "envs/pydev_1.yml"
    params:
    ¦   "01.pulled_reads"
    output:
    ¦   directory("01.pulled_reads/{tissue}")
    shell:"""

    mkdir 01.pulled_reads/{wildcards.tissue}

    store_regions=$(cat {input.bed_file} | awk -F'\t' '{{ print $1 ":" $2 "-" $3 }}')

    for i in $store_regions ; do
    ¦   samtools view -b -h {input.rna_file} ${{i}} > 01.pulled_reads/{wildcards.tissue}/${{i}}.bam ;
    done

    echo "This completed fine"

    """

rule samtools_sort:
    input:
    ¦   "01.pulled_reads/{tissue}/{i}.bam"
    params:
    ¦   "{i}"
    output:
    ¦   "01.pulled_reads/{tissue}/{i}.sorted.bam"
    shell:
    ¦   "samtools sort -T sorted_reads/{params}.tmp {input} > {output}"

rule samtools_index:
    input:
    ¦   "01.pulled_reads/{tissue}/{i}.sorted.bam"
    output:
    ¦   "01.pulled_reads/{tissue}/{i}.sorted.bam.bai"
    shell:
        "samtools index {input}"

rule string_tie_assembly:
    input:
    ¦   "01.pulled_reads/{tissue}/{i}.sorted.bam"
    output:
    ¦   "02.string_tie_assembly/{tissue}/{i}_assembly.gtf"
    shell:
        "stringtie {input} -f 0.0 -a 0 -m 50 -c 3.0 -f 0.0 -o {output}"


def trigger_aggregate(wildcards):
    checkpoint_output = checkpoints.pull_reads_for_BAM.get(**wildcards).output[0]

    x = expand("02.string_tie_assembly/{tissue}/{i}_assembly.merged.gtf",
    ¦   tissue = wildcards.tissue,
    ¦   i=glob_wildcards(os.path.join(checkpoint_output, "{i}.bam")).i)
    return x


#Aggregate function that triggers rule 
rule combine_all_gtf_things:
    input:
    ¦   trigger_aggregate
    output:
    ¦   "03.final_stuff/{tissue}.merged.gtf"
    shell:"""
    cat {input} > {output}
    """

命令执行完毕后，snakemake出于某种神秘原因返回(exited with non-zero exit code)。我可以看到文件中生成了输出，它看起来是正确的，所以我不确定为什么会引发此错误。

我生成的检查点是在此之后建模的： https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html

尚未回答的相关问题： Snakemake checkpoint (exited with non-zero exit code)

Answer 1

该问题似乎是由{tissue}中的通配符设置为目录引起的。至于为什么会抛出非零退出状态，我不确定。只需将{tissue}_dir附加到上面的路径即可解决此问题。

有关此问题的更多信息，请参见： https://bitbucket.org/snakemake/snakemake/issues/1303/snakemake-checkpoint-throws-exited-with

Answer 2

不确定这是否是问题，但是在执行mkdir之前，如果目录存在或mkdir 01.pulled_reads/{wildcards.tissue}不存在，01.pulled_reads将失败。

尝试将-p选项添加到mkidr，即mkdir -p 01.pulled_reads/{wildcards.tissue}

即使正确完成，Snakemake Checkpoint抛出（以非零退出代码退出）

2 个答案: