我结合了Singularity＆amp; Snakemake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之后模拟了我的管道。不使用Singularity的管道版本运行得非常好。使用Singularity的版本始终在第一个规则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logs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？