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我正在结合 Singularity 和 Snakemake 来为一些测序数据创建工作流程。我在这个 git 项目https://github.com/sci-f/snakemake.scif之后建模了我的管道。不使用 Singularity 的管道版本运行良好。使用 Singularity 的版本总是在第一条规则之后停止，并出现以下错误：

$ singularity run --bind data/raw_data/:/scif/data/ /gpfs/data01/heinzlab/home/cag104/bin/chip-seq-pipeline/chip-seq-pipeline-hg38.simg run snakemake all
[snakemake] executing /bin/bash /scif/apps/snakemake/scif/runscript all
Copying Snakefile to /scif/data
Copying config.yaml to /scif/data
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       all
        1       bowtie2_mapping
        1       create_bigwig
        1       create_tag_directories
        1       fastp
        1       fastqc
        1       quality_metrics
        1       samtools_index
        8

rule fastp:
    input: THP-1_PU1-cMyc_PU1_sc_S40_R1_001.fastq.gz
    output: fastp/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.fastp.fastq.gz, fastp_report/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.html, fastp_report/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.json
    log: logs/fastp/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.log
    jobid: 7
    wildcards: sample=THP-1_PU1-cMyc_PU1_sc_S40_R1_001

usage: scif run [-h] [cmd [cmd ...]]

positional arguments:
  cmd         app and optional arguments to target for the entry

optional arguments:
  -h, --help  show this help message and exit
Waiting at most 5 seconds for missing files.
MissingOutputException in line 16 of /scif/data/Snakefile:
Missing files after 5 seconds:
fastp/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.fastp.fastq.gz
fastp_report/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.html
fastp_report/THP-1_PU1-cMyc_PU1_sc_S40_R1_001.json
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Will exit after finishing currently running jobs.
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /scif/data/.snakemake/log/2018-04-06T224320.958604.snakemake.log

然而，该目录确实创建了 fastp 和 fastp_report 目录以及日志目录。我尝试将延迟增加到 50 秒，但我仍然得到同样的错误。

关于在这里尝试什么的任何想法？

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