Question

我打算将生物信息学管道转移到snakemake，因为我目前的管道是多个脚本的集合，越来越难以遵循。在教程和文档的基础上，snakemake似乎是管道管理的非常明确和有趣的选择。但是，我不熟悉Python，因为我主要使用bash和R，所以snakemake似乎难以学习：我正面临以下问题。

我有两个文件，sampleA_L001_R1_001.fastq.gz和sampleA_L001_R2_001.fastq.gz，wchich放在同一个目录sampleA中。我想使用cat命令合并这些文件。这实际上是一个测试运行：在实际情况下，每个样本我将有八个单独的FASTQ文件，应该以类似的方式合并。非常简单的工作，但我的代码有问题。

snakemake --latency-wait 20 --snakefile /home/users/me/bin/snakefile.txt

rule mergeFastq:
    input:
        reads1='sampleA/sampleA_L001_R1_001.fastq.gz',
        reads2='sampleA/sampleA_L001_R2_001.fastq.gz'
    output:
        reads1='sampleA/sampleA_R1.fastq.gz',
        reads2='sampleA/sampleA_R2.fastq.gz'
    message:
        'Merging FASTQ files...'
    shell:
        'cat {input.reads1} > {output.reads1}'
        'cat {input.reads2} > {output.reads2}'

-------------------------------------------------------------

Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1   mergeFastq
    1

Job 0: Merging FASTQ files...

Waiting at most 20 seconds for missing files.
Error in job mergeFastq while creating output files sampleA_R1.fastq.gz, sampleA_R2.fastq.gz.
MissingOutputException in line 5 of /home/users/me/bin/snakefile.txt:
Missing files after 20 seconds:
sampleA_R1.fastq.gz
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Removing output files of failed job mergeFastq since they might be corrupted: sampleA_R2.fastq.gz
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message.

正如您所看到的，我已经尝试了--latency-wait选项但没有成功。你有什么想法可能是我的问题的根源吗？文件路径是正确的，文件本身没有损坏，没问题。我也遇到了类似通配符的问题，所以在snakemake基础知识中肯定有一些我不理解的东西。

Answer 1

问题出在shell语句中，它连接成一个命令，生成一个文件＆＃34; sampleA / sampleA_R1.fastq.gzcat＆＃34;这就是为什么snakemake找不到的正确的输出。您可以使用以下语法：

rule mergeFastq:
    input:
        reads1='sampleA/sampleA_L001_R1_001.fastq.gz',
        reads2='sampleA/sampleA_L001_R2_001.fastq.gz'
    output:
        reads1='sampleA/sampleA_R1.fastq.gz',
        reads2='sampleA/sampleA_R2.fastq.gz'
    message:
        'Merging FASTQ files...'
    shell:"""
        cat {input.reads1} > {output.reads1}
        cat {input.reads2} > {output.reads2}
    """

不需要延迟等待选项。

snakemake

1 个答案: