如何解决WildcardError-没有为通配符提供任何值-Snakemake
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}"
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”。
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