STAR指数发行到步骤4

Question

我正在尝试使用 snakemake 在管道上索引参考基因组，我制定了这个规则：

rule reference_faidx_star:
    input:
        "../resources/reference/Qrob_PM1N.fa"
    output:
        "../resources/reference/ref/"
    threads: 1
    log: 
        "../results/logs/star/star_index.log"
    params:
        gtf= "../resources/reference/gff_gtf/Qrob_PM1N_genes_20161004.gtf"
    # resources:
    #     mem_mb=25000
    message:
        """
        INDEX STAR 
        """
    shell:
        "STAR --runMode genomeGenerate --runThreadN {threads} --genomeDir {output} --genomeFastaFiles {input} --sjdbGTFfile {params.gtf} --sjdbOverhang 149 --genomeSAindexNbases 12 " # Logging

起初一切正常，但在第 4 步出现中断。我的文件夹中只创建了 4 个文件：chrLength.txt、chrNameLength.txt、chrName.txt、chrStart.txt，终端显示为：

[Tue Apr 20 09:09:30 2021]
Job 4: 
        INDEX STAR 
        

Apr 20 09:09:30 ..... started STAR run
Apr 20 09:09:30 ... starting to generate Genome files
Apr 20 09:09:50 ... starting to sort Suffix Array. This may take a long time...
Apr 20 09:09:55 ... sorting Suffix Array chunks and saving them to disk...
/usr/bin/bash : ligne 1 :  7343 Processus arrêté      STAR --runMode genomeGenerate --runThreadN 1 --genomeDir ../resources/reference/ref/ --genomeFastaFiles ../resources/reference/Qrob_PM1N.fa --sjdbGTFfile ../resources/reference/gff_gtf/Qrob_PM1N_genes_20161004.gtf --sjdbOverhang 149 --genomeSAindexNbases 12 -limitGenomeGenerateRAM 25000000000
[Tue Apr 20 09:10:01 2021]
Error in rule reference_faidx_star:
    jobid: 4
    output: ../resources/reference/ref/
    log: ../results/logs/star/star_index.log (check log file(s) for error message)
    shell:
        STAR --runMode genomeGenerate --runThreadN 1 --genomeDir ../resources/reference/ref/ --genomeFastaFiles ../resources/reference/Qrob_PM1N.fa --sjdbGTFfile ../resources/reference/gff_gtf/Qrob_PM1N_genes_20161004.gtf --sjdbOverhang 149 --genomeSAindexNbases 12 
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

我不明白这条规则有什么问题，我没有写在bash？

希望你能帮助我。谢谢，祝你有美好的一天！

Answer 1

这个问题与Snakemake无关，与Python无关。日志清楚地向您显示 bash 在 Snakemake 运行管道时执行的确切命令：

STAR --runMode genomeGenerate --runThreadN 1 --genomeDir ../resources/reference/ref/ --genomeFastaFiles ../resources/reference/Qrob_PM1N.fa --sjdbGTFfile ../resources/reference/gff_gtf/Qrob_PM1N_genes_20161004.gtf --sjdbOverhang 149 --genomeSAindexNbases 12 -limitGenomeGenerateRAM 25000000000

执行过程中出现了错误，可能是内存不足，磁盘问题等。在bash中尝试运行此命令并检查return代码：可能会给你更多关于发生的事情的信息。

一个有用的 Snakemake lifehack 是使用 --printshellcmds 标志：这将明确向您显示 Snakemake 运行s 的所有命令。您可以手动重复这些命令，保留所有临时文件，然后定位问题。

STAR指数发行到步骤4

STAR index issues to the step 4

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snakemake