许多Trimmomatic修整参数在Snakemake包装器中不起作用

编程问答 2022-07-20

问题描述

以前，我的Trimmomatic shell命令包含以下修剪器：

ILLUMINACLIP：adapters.fa：2：30：10领先：3训练：3滑动窗口：4：15 MINLEN：36

对于Snakemake wrapper for Trimmomatic，只有LEADING:3和MINLEN:36在params: trimmer中起作用：

rule trimming:
    input:
        r1 = lambda wildcards: getHome(wildcards.sample)[0],r2 = lambda wildcards: getHome(wildcards.sample)[1]
    output:
        r1 = os.path.join(dirs_dict["TRIM_DIR"],config["TRIM_TOOL"],"{sample}_R1_trim_paired.fastq.gz"),r1_unpaired = os.path.join(dirs_dict["TRIM_DIR"],"{sample}_R1_trim_unpaired.fastq.gz"),r2 = os.path.join(dirs_dict["TRIM_DIR"],"{sample}_R2_trim_paired.fastq.gz"),r2_unpaired = os.path.join(dirs_dict["TRIM_DIR"],"{sample}_R2_trim_unpaired.fastq.gz")
    log: os.path.join(dirs_dict["LOG_DIR"],"{sample}.log")
    threads: 32
    params:
    # list of trimmers (see manual)
        trimmer=["LEADING:3","MINLEN:36"],# optional parameters
        extra="",compression_level="-9"
    resources:
    mem = 1000,time = 120
    message: """--- Trimming FASTQ files with Trimmomatic."""
    wrapper:
    "0.64.0/bio/trimmomatic/pe"

尝试使用任何其他参数（ILLUMINACLIP:adapters.fa:2:30:10 TRAILING:3 SLIDINGWINDOW:4:15）时失败。

例如，仅尝试TRAILING:3：

rule trimming:
    input:
        r1 = lambda wildcards: getHome(wildcards.sample)[0],"{sample}.log")
    threads: 32
    params:
    # list of trimmers (see manual)
        trimmer=["TRAILING:3"],time = 120
    message: """--- Trimming FASTQ files with Trimmomatic."""
    wrapper:
    "0.64.0/bio/trimmomatic/pe"

导致以下错误：

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
        1   qc_before_align_r1
        1

[Mon Sep 14 13:42:08 2020]
Job 0: --- Quality check of raw data with FastQC before alignment.

Activating conda environment: /home/moldach/wrappers/.snakemake/conda/975fb1fd
Activating conda environment: /home/moldach/wrappers/.snakemake/conda/975fb1fd
Skipping ' 2> logs/fastqc/before_align/MTG324_R1.log' which didn't exist,or Couldn't be read
Failed to process file MTG324_R1_trim_paired.fastq.gz
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Ran out of data in the middle of a fastq entry.  Your file is probably truncated
        at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:179)
        at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)
        at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:77)
        at java.base/java.lang.Thread.run(Thread.java:834)
mv: cannot stat ‘/tmp/tmpsnncjthh/MTG324_R1_trim_paired_fastqc.html’: No such file or directory
Traceback (most recent call last):
  File "/home/moldach/wrappers/.snakemake/scripts/tmpp34b98yj.wrapper.py",line 47,in <module>
    shell("mv {html_path:q} {snakemake.output.html:q}")
  File "/home/moldach/anaconda3/envs/snakemake/lib/python3.7/site-packages/snakemake/shell.py",line 205,in __new__
    raise sp.CalledProcessError(retcode,cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail;  mv /tmp/tmpsnncjthh/MTG324_R1_trim_paired_fastqc.html qc/fastQC/before_align/MTG324_R1_trim_paired_fastqc.html' returned non-zero exit status $
[Mon Sep 14 13:45:16 2020]
Error in rule qc_before_align_r1:
    jobid: 0
    output: qc/fastQC/before_align/MTG324_R1_trim_paired_fastqc.html,qc/fastQC/before_align/MTG324_R1_trim_paired_fastqc.zip
    log: logs/fastqc/before_align/MTG324_R1.log (check log file(s) for error message)
    conda-env: /home/moldach/wrappers/.snakemake/conda/975fb1fd

RuleException:
CalledProcessError in line 181 of /home/moldach/wrappers/Trim:
Command 'source /home/moldach/anaconda3/bin/activate '/home/moldach/wrappers/.snakemake/conda/975fb1fd'; set -euo pipefail;  python /home/moldach/wrappers/.snakemake/scripts/tmpp34b98yj.wrapper.py' retu$
  File "/home/moldach/anaconda3/envs/snakemake/lib/python3.7/site-packages/snakemake/executors/__init__.py",line 2189,in run_wrapper
  File "/home/moldach/wrappers/Trim",line 181,in __rule_qc_before_align_r1
  File "/home/moldach/anaconda3/envs/snakemake/lib/python3.7/site-packages/snakemake/executors/__init__.py",line 529,in _callback
  File "/home/moldach/anaconda3/envs/snakemake/lib/python3.7/concurrent/futures/thread.py",line 57,in run
  File "/home/moldach/anaconda3/envs/snakemake/lib/python3.7/site-packages/snakemake/executors/__init__.py",line 515,in cached_or_run
  File "/home/moldach/anaconda3/envs/snakemake/lib/python3.7/site-packages/snakemake/executors/__init__.py",line 2201,in run_wrapper
Shutting down,this might take some time.
Exiting because a job execution Failed. Look above for error message

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