WildcardError-没有为通配符提供任何值-Snakemake

问题描述

我真的迷失了解决该错误的确切方法。 我正在运行snakemake来执行一些对齐后质量检查。 我的代码如下：

SAMPLES = ["Exome_Tumor_sorted_mrkdup_bqsr","Exome_Norm_sorted_mrkdup_bqsr","WGS_Tumor_merged_sorted_mrkdup_bqsr","WGS_Norm_merged_sorted_mrkdup_bqsr"]

rule all:
    input:
        expand("post-alignment-qc/flagstat/{sample}.txt",sample=SAMPLES),expand("post-alignment-qc/CollectInsertSizeMetics/{sample}.txt",expand("post-alignment-qc/CollectAlignmentSummaryMetrics/{sample}.txt",expand("post-alignment-qc/CollectGcBiasMetrics/{sample}_summary.txt",samples=SAMPLES) # this is the problem causing line

rule flagstat:
    input:
         bam = "align/{sample}.bam"
    output:
          "post-alignment-qc/flagstat/{sample}.txt"
    log:
       err='post-alignment-qc/logs/flagstat/{sample}_stderr.err'
    shell:
         "samtools flagstat {input} > {output} 2> {log.err}"


rule CollectInsertSizeMetics:
    input:
         bam = "align/{sample}.bam"
    output:
          txt="post-alignment-qc/CollectInsertSizeMetics/{sample}.txt",pdf="post-alignment-qc/CollectInsertSizeMetics/{sample}.pdf"
    log:
       err='post-alignment-qc/logs/CollectInsertSizeMetics/{sample}_stderr.err',out='post-alignment-qc/logs/CollectInsertSizeMetics/{sample}_stdout.txt'

    shell:
         "gatk CollectInsertSizeMetrics -I {input} -O {output.txt} -H {output.pdf} 2> {log.err}"

rule CollectAlignmentSummaryMetrics:
    input:
         bam = "align/{sample}.bam",genome= "references/genome/ref_genome.fa"
    output:
          txt="post-alignment-qc/CollectAlignmentSummaryMetrics/{sample}.txt",log:
       err='post-alignment-qc/logs/CollectAlignmentSummaryMetrics/{sample}_stderr.err',out='post-alignment-qc/logs/CollectAlignmentSummaryMetrics/{sample}_stdout.txt'

    shell:
         "gatk CollectAlignmentSummaryMetrics -I {input.bam} -O {output.txt} -R {input.genome} 2> {log.err}"

rule CollectGcBiasMetrics:
    input:
         bam = "align/{sample}.bam",genome= "references/genome/ref_genome.fa"

    output:
          txt="post-alignment-qc/CollectGcBiasMetrics/{sample}_metrics.txt",CHART="post-alignment-qc/CollectGcBiasMetrics/{sample}_metrics.pdf",S="post-alignment-qc/CollectGcBiasMetrics/{sample}_summary.txt"

    log:
       err='post-alignment-qc/logs/CollectGcBiasMetrics/{sample}_stderr.err',out='post-alignment-qc/logs/CollectGcBiasMetrics/{sample}_stdout.txt'

    shell:
         "gatk CollectGcBiasMetrics -I {input.bam} -O {output.txt} -R {input.genome} -CHART = {output.CHART} "
         "-S {output.S} 2> {log.err}"

错误消息显示以下内容：

WildcardError in line 9 of Snakefile:
No values given for wildcard 'sample'.
  File "Snakefile",line 9,in <module>

在上面的代码中，我已经指出了引起问题的原因。当我简单地删除此行时，一切都会正常运行。我真的很困惑，因为我几乎复制并粘贴了每个规则，而这是唯一会引起问题的规则。

如果有人指出我做错了，我将非常感激！

干杯！

解决方法

似乎可能是拼写错误-在突出显示的行中，您写了samples=SAMPLES，但通配符称为{sample}，而没有“ s”。