缺少所有规则的输入文件，但应该存在

如何解决缺少所有规则的输入文件，但应该存在

在运行我的 Snakemake 管道时，我收到以下错误：

MissingInputException in line 19 of Snakefile:
Missing input files for rule all:
results/hisat2/featureCounts/all.fixed.featureCounts
results/star/featureCounts/all.fixed.featureCounts

下面是我的主要 Snakefile。之后，我有与此错误相关的 rules/featurecounts.smk。

似乎我有一个规则定义可以防止这个错误。

Snakefile：

configfile: "config.yaml"

units = pd.read_table(config["units"],dtype=str).set_index(["sample","unit"],drop=False)
units.index = units.index.set_levels([i.astype(str) for i in units.index.levels])  # enforce str in index
aligners=config["params"]["aligners"].split(",")
print("Aligners:",aligners)


##### target rules #####

rule all:
    input:
        "qc/multiqc_report_pretrim.html","qc/multiqc_report_posttrim.html",expand("qc/multiqc_report_{aligner}.html",aligner=aligners),expand("results/{aligner}/featureCounts/all.fixed.featureCounts",aligner=aligners)

##### setup report #####

report: "report/workflow.rst"


##### load rules #####

#include: "rules/common.smk"
include: "rules/qc.smk"
include: "rules/trim.smk"
include: "rules/align.smk"
include: "rules/featurecounts.smk"

featurecounts.smk 文件

rule featurecounts_onefile_star:
    input:
        sam=expand("star/{unit.sample}.{unit.unit}/{unit.sample}.{unit.unit}_Aligned.sortedByCoord.out.bam",unit=units.itertuples()),annotation=config["ref"]["annotation"],fasta=config["ref"]["genomefa"]     # implicitly sets the -G flag
    output:
        multiext("results/star/featureCounts/all",".featureCounts",".featureCounts.summary",".featureCounts.jcounts")
    log:
        "logs/star/featurecount/all.log"
    params:
        tmp_dir="",# implicitly sets the --tmpDir flag
        r_path="",# implicitly sets the --Rpath flag
        #extra="-p -C -t exon -g gene_id --extraAttributes gene_name,transcript_id,transcript_name"   #-p to count fragments instead of reads,-C to not count fragments if mapped to different chrs,-t exon (only consider exons,-g look at the gene_id field to get the feature name
        extra="{}".format(config["params"]["featurecounts"])
    threads: 8
    resources: time_min=220,mem_mb=20000,cpus=8
    wrapper:
        "0.69.0/bio/subread/featurecounts"

rule featurecounts_onefile_hisat2:
    input:
        sam=expand("hisat2/{unit.sample}.{unit.unit}.sorted.bam",fasta=config["ref"]["genomefa"]     # implicitly sets the -G flag
    output:
        multiext("results/hisat2/featureCounts/all",".featureCounts.jcounts")
    log:
        "logs/hisat2/featurecount/all.log"
    params:
        tmp_dir="",cpus=8
    wrapper:
        "0.69.0/bio/subread/featurecounts"

rule fix_featurecounts:
    input:
        "results/{aligner}/featureCounts/all.featureCounts"
    output:
        "results/{aligner}/featureCounts/all.fixed.featureCounts"
    log:
        "logs/{aligner}/featurecount/fix.log"
    threads: 1
    resources: time_min=220,mem_mb=2000,cpus=1
    shell:
        "python3 ../scripts/fix_featurecounts_output.py -f {input} -c 2 > {output} 2> {log}"