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slurm - Snakemake 在使用 --profile slurm 时给出 InputFunctionException

问题描述

我正在使用snakemake 创建一个管道来调用纳米孔测序数据中的甲基化。我已经使用 --dryrun 选项运行了蛇形，并且成功构建了 dag。但是当我添加选项 --profile slurm 时，我收到以下错误：

(nanopolish) [danielle.perley@talonhead2 nanopolish-CpG-calling]$ snakemake -np --use-conda --profile slurm test_data/20-001-002/20-001-002_fastq_pass.gz

Building DAG of jobs...
Job counts:
    count   jobs
    1   combine_tech_reps
    1
InputFunctionException in line 32 of /home/danielle.perley/nanopolish-CpG-calling/Snakefile:
Error:
  SyntaxError: invalid syntax (<string>, line 1)
Wildcards:
  sample=20-001-002
Traceback:

  File "/home/danielle.perley/miniconda3/envs/nanopolish/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 115, in run_jobs
  File "/home/danielle.perley/miniconda3/envs/nanopolish/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 120, in run
  File "/home/danielle.perley/miniconda3/envs/nanopolish/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 131, in _run
  File "/home/danielle.perley/miniconda3/envs/nanopolish/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 151, in printjob
  File "/home/danielle.perley/miniconda3/envs/nanopolish/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 137, in printjob

第 33 行是我的蛇文件中的规则 combine_tech_reps。（我只在这里展示我的蛇文件的第一部分）

from snakemake.utils import validate
import pandas as pd
import os.path
import glob

configfile: "config.yaml"

samples_df = pd.read_table(config["samples"],sep = '\t')
samples_df = samples_df.set_index("Sample")
samples = list(samples_df.index.unique())


wildcard_constraints:
    sample = "|".join(samples)
         
def get_fast5(wildcards):
      
    f5 = glob.glob(os.path.join(config["raw_data"],wildcards.sample,"2*","fast5_pass"))
    return(f5)

localrules: all,build_index

rule all:
    input: 
        expand("results/Methylation/{sample}_frequency.tsv",sample=samples),
        expand("results/alignments/{sample}_flagstat.txt",sample=samples),
        expand("resources/QC/{sample}_pycoQC.json",sample=samples),
        expand("results/QC/{sample}_pycoQC.html",sample=samples),
        "report/multiQC.html"


rule combine_tech_reps:
    input:
        fqs = lambda wildcards: glob.glob(os.path.join(config["raw_data"],"{sample}","2*","{sample}_fastq_pass.gz").format(sample=wildcards.sample))

    output:
        fq = os.path.join(config["raw_data"],"{sample}","{sample}_fastq_pass.gz")

    shell: """
        zcat {input} > {output}
    """

我在目录中有一个 slurm 配置文件：~/.config/snakemake/slurm/config.yaml

jobs: 10
cluster: "sbatch -p talon -t {resources.time} --mem={resources.mem} -c {resources.cpus} -o logs_slurm/{rule}_{wildcards} -e logs_slurm/{rule}_{wildcards}"
default-resources: [cpus=1, mem=2000, time=10:00]
use-conda: true

我真的很想在我们的 HPC 上使用这个管道，但我不确定是什么导致了这个错误。

标签： slurmsnakemake

解决方案

在这篇文章的帮助下，我能够解决我的问题：

InputFunctionException：解析时出现意外的 EOF

通过添加详细标志：

snakemake -np --verbose --use-conda --profile slurm test_data/20-001-002/20-001-002_fastq_pass.gz

我可以看到snakemake的默认资源有问题：

10:00
   ^

更改我的 config.yaml 文件的默认资源行：

default-resources: [cpus=1, mem=2000, time=600]

删除了错误。

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