Snakemake on cluster error: 'Wildcards' object has no attribute 'output'

Question

当我将 Snakemake 提交到我的集群时，我运行遇到了 'Wildcards' object has no attribute 'output' 的错误，类似于之前的问题 'Wildcards' object has no attribute 'output' .我想知道您是否对如何使其与集群兼容有任何建议？

虽然我的规则 annotate_snps 在本地测试时有效，但我在集群上收到以下错误：

    input: results/CI226380_S4/vars/CI226380_S4_bwa_H37Rv_gatk.vcf.gz
    output: results/CI226380_S4/vars/CI226380_S4_bwa_H37Rv_gatk_rename.vcf.gz, results/CI226380_S4/vars/CI226380_S4_bwa_H37Rv_gatk_tmp.vcf.gz, results/CI226380_S4/vars/CI226380_S4_bwa_H37Rv_gatk_ann.vcf.gz
    log: results/CI226380_S4/vars/CI226380_S4_bwa_H37Rv_annotate_snps.log
    jobid: 1139
    wildcards: samp=CI226380_S4, mapper=bwa, ref=H37Rv

WorkflowError in line 173 of /oak/stanford/scg/lab_jandr/walter/tb/mtb/workflow/Snakefile:
'Wildcards' object has no attribute 'output'

我的规则定义为：

rule annotate_snps: 
  input:
    vcf='results/{samp}/vars/{samp}_{mapper}_{ref}_gatk.vcf.gz'
  log: 
    'results/{samp}/vars/{samp}_{mapper}_{ref}_annotate_snps.log'
  output:
    rename_vcf=temp('results/{samp}/vars/{samp}_{mapper}_{ref}_gatk_rename.vcf.gz'),
    tmp_vcf=temp('results/{samp}/vars/{samp}_{mapper}_{ref}_gatk_tmp.vcf.gz'),
    ann_vcf='results/{samp}/vars/{samp}_{mapper}_{ref}_gatk_ann.vcf.gz'
  params: 
    bed=config['bed_path'],
    vcf_header=config['vcf_header']
  shell:
    '''
    # Rename Chromosome to be consistent with snpEff/Ensembl genomes.
    zcat {input.vcf}| sed 's/NC_000962.3/Chromosome/g' | bgzip > {output.rename_vcf}
    tabix {output.rename_vcf}

    # Run snpEff
    java -jar -Xmx8g {config[snpeff]} eff {config[snpeff_db]} {output.rename_vcf} -dataDir {config[snpeff_datapath]} -noStats -no-downstream -no-upstream -canon > {output.tmp_vcf}

    # Also use bed file to annotate vcf
    bcftools annotate -a {params.bed} -h {params.vcf_header} -c CHROM,FROM,TO,FORMAT/PPE {output.tmp_vcf} > {output.ann_vcf}

    '''

在此先感谢您！

Answer 1

除了多次调用 config 的内容外，原始规则定义似乎是一致的，例如config[snpeff].

要检查的一件事是单机和集群上的配置定义是否相同，如果不相同，可能会有一些令人困惑的内容snakemake，例如如果不知何故 config[snpeff] == "wildcards.output"（或类似的东西）。

Snakemake on cluster error: 'Wildcards' object has no attribute 'output'

Snakemake on cluster error: 'Wildcards' object has no attribute 'output'

wildcard

cluster-computing

snakemake