Snakemake写入列表到文件时触发MissingOutputException问题排查

在使用Snakemake规则时遇到MissingOutputException异常，尝试通过Python代码将config.yaml中的列表写入scaffolds.list文件，但Snakemake持续报错。相关代码如下：

# --- Importing Configuration Files --- #

configfile: "config.yaml"

# -------------------------------------------------

scaffolds = config["Scaffolds"]

localrules: all, MakeScaffoldList

# -------------------------------------------------

rule all:
    input:
        LIST = "scaffolds.list"

# -------------------------------------------------

rule MakeScaffoldList:
    output:
        LIST = "scaffolds.list"
    params:
        SCAFFOLDS = scaffolds
    run:
        """
        with open(output.LIST, 'w') as f:
            for line in params.SCAFFOLDS:
                f.write(f"{line}\n")
        """

错误信息：

[Thu Nov 17 14:08:33 2022]
localrule MakeScaffoldList:
    output: scaffolds.list
    jobid: 1
    resources: mem_mb=27200, disk_mb=1000, tmpdir=/scratch, account=snic2022-22-156, partition=core, time=12:00:00, threads=4

MissingOutputException in line 37 of test.smk:
Job Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
scaffolds.list completed successfully, but some output files are missing. 0
Exiting because a job execution failed. Look above for error message

• 核心问题：run块的代码被当作shell命令执行，而非Python代码
  Snakemake中，run块若用三重双引号包裹内容，会被识别为shell命令执行。你写的Python代码被当成shell命令运行，自然不会生成目标文件，触发MissingOutputException。

• 修复步骤
  移除run块内的三重双引号，直接编写Python代码：

  rule MakeScaffoldList:
      output:
          LIST = "scaffolds.list"
      params:
          SCAFFOLDS = scaffolds
      run:
          with open(output.LIST, 'w') as f:
              for line in params.SCAFFOLDS:
                  f.write(f"{line}\n")
  

• 额外验证项

  1. 确认config.yaml中的Scaffolds是合法列表格式，示例：

     Scaffolds:
       - scaffold_1
       - scaffold_2
       - scaffold_3
     

  2. 若在集群共享文件系统运行，可尝试添加--latency-wait 10参数规避文件系统延迟误判，但这是临时方案，核心仍需修复run块的代码执行方式。

内容的提问来源于stack exchange，提问作者Valentina