如何解决许多Trimmomatic修整参数在Snakemake包装器中不起作用
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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