使用奇异性在snakemake中运行docker管道，但未指定奇异性exec docker：//

Question

我正在尝试将Docker上现有管道中的脚本绑定到我的snakemake管道中。我使用奇异性设置了docker管道，并且可以正常工作。例如，

singularity exec docker://mypipeline some_command.sh file.bam out_file.bam

当我在命令行上交互式运行时，效果很好。同样，当我将完全相同的命令合并到我的Snakefile中时，它也可以工作：

rule myrule:
        input:
                "file.bam"
        output:
                "out_file.bam"
        shell:
                "singularity exec docker://mypipeline some_command.sh {input} {output}"

但是，当我尝试按照本教程https://reproducibility.sschmeier.com/container/index.html#using-a-container-in-our-workflow将容器合并到我的工作流中时，如下所示

singularity: "docker://mypipeline"

rule myrule:
    input:
            "file.bam"
    output:
            "out_file.bam"
    shell:
            "some_command.sh {input} {output}"

然后运行snakemake -p --use-singularity --cores 1，我得到以下输出

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       myrule
        1

[Sun May 17 15:28:11 2020]
rule myrule:
    input: file.bam
    output: out_file.bam
    jobid: 0

some_command.sh file.bam out_file.bam
Activating singularity image myImage.simg

然后，我收到一份很长的报告，不确定该如何处理，然后出现此错误消息

Waiting at most 5 seconds for missing files.
MissingOutputException in line 3 of Snakefile:
Job completed successfully, but some output files are missing. Missing files after 5 seconds:
out_file.bam
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2020-05-17T152810.484310.snakemake.log

我的问题：

• 为什么一个起作用而另一个不起作用/如何使最后一个示例起作用？
• 提前声明singularity: "docker://...是好的做法还是没关系？

Answer 1

错误消息表明奇异性命令已成功执行，但snakemake没有看到输出文件。代码中显示的输出文件out_file.bam是否与实际使用的文件相同，或者您删除了一些文件路径？我建议将--verbose标志添加到snakemake并检查snakemake执行的实际奇点命令。