0

我知道这是一个常见错误，我已经检查了其他帖子，但它并没有解决我的问题。我想使用与我使用相同的方式用于SortMeRNArule( ) 的数据库的名称。但很显然，我做不到。rRNAdb=config["rRNA_database"]version=config["genome_version"]

SyntaxError:
Not all output, log and benchmark files of rule SortMeRNA contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file

......

import glob
import os

configfile : "config.json"


#################### GLOBAL VARIABLES #######################

OUTDIR = os.path.abspath(config["outdir"])


# ID NGS
idNGS = config["idNGS"]

# Fichiers FASTQ
DIR_FASTQ = config["dir_fastq"]

## PARAMETERS TRIMMOMATIC
w = config["w"]
Q = config["Q"]
m = config["m"]

## Bowtie2 database
BWT2_DB = config["BWT2_DB"]

## Templates multiQC
DIR_TPL = config["DIR_TPL"]


#### VERSIONS genomes and database ####
version = config["genome_version"]
rRNAdb = config["rRNA_database"]


####################### FASTQ FILES #########################

def list_samples(DIR_FASTQ): # create list with all sample names from fastq directory
    SAMPLES=[]
    for file in glob.glob(DIR_FASTQ+"/*.fastq.gz"):
        base=os.path.basename(file)
        sample=(base.replace('.fastq.gz', ''))
        SAMPLES.append(sample)
    return(SAMPLES)

SAMPLES = list_samples(DIR_FASTQ)


########################## RULES ############################

rule all:
    input:
        OUTDIR+"/multiQC/multiQC-PL09_"+idNGS+".html",
        OUTDIR+"/multiQC/multiQC-PL21_"+idNGS+".html"


rule fastQC:
    input: 
        DIR_FASTQ+"/{sample}.fastq.gz"
    output: 
        "{OUTDIR}/FastQC/{sample}_fastqc.zip",
        "{OUTDIR}/FastQC/{sample}_fastqc.html"
    threads:
        16
    shell:
        """
        fastqc {input} -o {OUTDIR}/FastQC/
        """ 

rule trimmomatic:
    input:
        DIR_FASTQ+"/{sample}.fastq.gz"
    output:
        trim_out="{OUTDIR}/Trimmomatic/{sample}_SL-{w}-{Q}_Min-{m}.fastq.gz",
        trim1_out="{OUTDIR}/Trimmomatic/{sample}_SL-{w}-{Q}_Min-{m}.stdout",
        trim1_err="{OUTDIR}/Trimmomatic/{sample}_SL-{w}-{Q}_Min-{m}.stderr"
    threads:
        16
    shell:
        "trimmomatic SE -phred33 {input} {output.trim_out} SLIDINGWINDOW:{w}:{Q} MINLEN:{m} > {output.trim1_out} 2> {output.trim1_err}"


rule Bowtie2:
    input:
        fasta_trim="{OUTDIR}/Trimmomatic/{sample}_SL-"+str(w)+"-"+str(Q)+"_Min-"+str(m)+".fastq.gz"
    output:
        BWT2_ERR="{OUTDIR}/Bowtie2/{sample}_SL-{w}-{Q}_Min-{m}_bowtie2_{version}.stderr",
        BWT2_SAM=temp("{OUTDIR}/Bowtie2/{sample}_SL-{w}-{Q}_Min-{m}_bowtie2_{version}.sam"),
        BWT2_BAM=temp("{OUTDIR}/Bowtie2/{sample}_SL-{w}-{Q}_Min-{m}_bowtie2_{version}.bam"),
        BWT2_BAM_SORTED="{OUTDIR}/Bowtie2/{sample}_SL-{w}-{Q}_Min-{m}_bowtie2_{version}.sorted.bam"
    threads:
        16
    shell:
        """
        bowtie2 -x {BWT2_DB} -U {input} 2> {output.BWT2_ERR} > {output.BWT2_SAM}
        samtools view -bS -o {output.BWT2_BAM} {output.BWT2_SAM}
        samtools sort {output.BWT2_BAM} -o {output.BWT2_BAM_SORTED}
        samtools index {output.BWT2_BAM_SORTED}
        """


rule copy_to_pigz: # we just copy fastq files to gunzip them and use them in sortMeRNA, this way we don't touch the original ones
    input:
        DIR_FASTQ+"/{sample}.fastq.gz"
    output:
        "{OUTDIR}/temp/{sample}.fastq.gz" # this temp directory will be deleted at the end of the pipeline in multiQC rule
    shell:
        "cp {input} {output}"


rule SortMeRNA:
    input:
        "OUTDIR/temp/{sample}.fastq.gz"
    output:
        fasta_pigz=temp("{OUTDIR}/temp/{sample}.fastq"),
        blast="{OUTDIR}/SortMeRNA/{sample}.fastq_SortMeRNA_{rRNAdb}.blast",
        log="{OUTDIR}/SortMeRNA/{sample}.fastq_SortMeRNA_{rRNAdb}.log"
    params:
        prefixSortMeRNA="{OUTDIR}/SortMeRNA/{sample}.fastq_SortMeRNA_{rRNAdb}",
        sortmerna_DB=config["SORTMERNA_DB"]
    shell:
        """
        pigz -d -k {input}
        sortmerna --ref {params.sortmerna_DB} --reads {output.fasta_pigz} --aligned {params.prefixSortMeRNA} --blast '1' --log TRUE
        """


rule multiQC:
    input: 
        expand(OUTDIR+"/FastQC/{sample}_fastqc.zip", sample=SAMPLES),
        expand(OUTDIR+"/Trimmomatic/{sample}_SL-"+str(w)+"-"+str(Q)+"_Min-"+str(m)+".fastq.gz", sample=SAMPLES),
        expand(OUTDIR+"/Trimmomatic/{sample}_SL-"+str(w)+"-"+str(Q)+"_Min-"+str(m)+".stdout", sample=SAMPLES),
        expand(OUTDIR+"/Trimmomatic/{sample}_SL-"+str(w)+"-"+str(Q)+"_Min-"+str(m)+".stderr", sample=SAMPLES),
        expand(OUTDIR+"/Bowtie2/{sample}_SL-"+str(w)+"-"+str(Q)+"_Min-"+str(m)+"_bowtie2_"+version+".stderr", sample=SAMPLES),
        expand(OUTDIR+"/SortMeRNA/{sample}.fastq_SortMeRNA_"+rRNAdb+".blast", sample=SAMPLES),
        expand(OUTDIR+"/SortMeRNA/{sample}.fastq_SortMeRNA_"+rRNAdb+".log", sample=SAMPLES),
        tpl_plNGS=DIR_TPL+"/template-PL-NGS_multiqc_config.yaml",
        tpl_plBioinfo=DIR_TPL+"/template-PL-Bioinfo_multiqc_config.yaml"
    output:
        rap_plNGS="{OUTDIR}/multiQC/multiQC-PL09_{idNGS}.html",
        rap_plBioinfo="{OUTDIR}/multiQC/multiQC-PL21_{idNGS}.html"
    shell:
        """
        sed -e "s/ID_NGS_HERE/{idNGS}/g" < {input.tpl_plNGS} > {OUTDIR}/multiQC/PL-NGS_multiqc_config.yaml
        sed -e "s/ID_NGS_HERE/{idNGS}/g" < {input.tpl_plBioinfo} > {OUTDIR}/multiQC/PL-Bioinfo_multiqc_config.yaml
        multiqc -c {OUTDIR}/multiQC/PL-NGS_multiqc_config.yaml -n {output.rap_plNGS} {OUTDIR}/
        multiqc -c {OUTDIR}/multiQC/PL-Bioinfo_multiqc_config.yaml -n {output.rap_plBioinfo} {OUTDIR}/
        rm -r {OUTDIR}/temp
        """

onsuccess:
    shell("date '+%d/%m/%Y %H:%M:%S' > time_end_RNAseq.txt")

是因为我在规则中使用它params而不是在这条规则中吗？因为在规则中，在规则中使用它似乎不是问题，而不是在......outputSortMeRNAinputsversionBowtieoutputsinput

4

1 回答 1

1

所有output文件都需要具有相同的通配符，否则会导致在解决作业依赖项时发生冲突。并非所有文件output:都有{rRNAdb}通配符，这导致了这个问题。例如，如果您有两个{rRNAdb}值，则两者都将写入 file "{OUTDIR}/temp/{sample}.fastq"，而这是 snakemake 正确不允许的。

rule SortMeRNA:
    input:
        "OUTDIR/temp/{sample}.fastq.gz"
    output:
        fasta_pigz=temp("{OUTDIR}/temp/{sample}.fastq"),
        blast="{OUTDIR}/SortMeRNA/{sample}.fastq_SortMeRNA_{rRNAdb}.blast",
        log="{OUTDIR}/SortMeRNA/{sample}.fastq_SortMeRNA_{rRNAdb}.log"
        """

PS - 看来您正在将变量OUTDIR与通配符混合，这将导致一些其他错误。

于 2020-01-20T16:08:37.143 回答