我正在研究蛇形设计,以便为我的工作做准备。 我的输入文件是(例如fastq文件示例)
/project/ateeq/PROJECT/snakemake-example/raw_data/H667-1_R1.fastq.gz
/project/ateeq/PROJECT/snakemake-example/raw_data/H667-1_R2.fastq.gz
/project/ateeq/PROJECT/snakemake-example/raw_data/H667-2_R1.fastq.gz
/project/ateeq/PROJECT/snakemake-example/raw_data/H667-2_R2.fastq.gz
我编写了以下代码,用于使用FastP修剪数据
"""
Author: Dave Amir
Affiliation: St Lukes
Aim: A simple Snakemake workflow to process paired-end stranded RNA-Seq.
Date: 11 June 2015
Run: snakemake -s snakefile
Latest modification:
- todo
"""
# This should be placed in the Snakefile.
##-----------------------------------------------##
## Working directory ##
## Adapt to your needs ##
##-----------------------------------------------##
BASE_DIR = "/project/ateeq/PROJECT"
WDIR = BASE_DIR + "/snakemake-example"
workdir: WDIR
#message("The current working directory is " + WDIR)
##--------------------------------------------------------------------------------------##
## Variables declaration
## Declaring some variables used by topHat and other tools...
## (GTF file, INDEX, chromosome length)
##--------------------------------------------------------------------------------------##
INDEX = BASE_DIR + "/ref_files/hg19/assembly/"
GTF = BASE_DIR + "/hg19/Hg19_CTAT_resource_lib/ref_annot.gtf"
CHR = BASE_DIR + "/static/humanhg19.annot.csv"
FASTA = BASE_DIR + "/ref_files/hg19/assembly/hg19.fasta"
##--------------------------------------------------------------------------------------##
## The list of samples to be processed
##--------------------------------------------------------------------------------------##
SAMPLES, = glob_wildcards("/project/ateeq/PROJECT/snakemake-example/raw_data/{smp}_R1.fastq.gz")
NB_SAMPLES = len(SAMPLES)
for smp in SAMPLES:
message:("Sample " + smp + " will be processed")
##--------------------------------------------------------------------------------------##
## Our First rule - sample trimming
##--------------------------------------------------------------------------------------##
rule final:
input: expand("/project/ateeq/PROJECT/snakemake-example/trimmed/{smp}_R1_trimmed.fastq", smp=SAMPLES)
rule trimming:
input: fwd="/project/ateeq/PROJECT/snakemake-example/raw_data/{smp}_R1.fastq.gz",rev="/project/ateeq/PROJECT/snakemake-example/raw_data/{smp}_R2.fastq.gz"
output: fwd="/project/ateeq/PROJECT/snakemake-example/trimmed/{smp}_R1_trimmed.fastq", rev="/project/ateeq/PROJECT/snakemake-example/trimmed/{smp}_R2_trimmed.fastq", rep="/project/ateeq/PROJECT/snakemake-example/report/{smp}.html"
threads: 30
message: """--- Trimming."""
shell: """
fastp -i {input.fwd} -I {input.rev} -o {output.fwd} -O {output.rev} --detect_adapter_for_pe --disable_length_filtering --correction --qualified_quality_phred 30 --thread 16 --html {output.rep} --report_title "Fastq Quality Control Report" &>>{input.fwd}.log
"""
我在运行管道时显示以下错误
MissingOutputException in line 51 of /project/ateeq/PROJECT/snakemake-example/snakefile:
Missing files after 5 seconds:
/project/ateeq/PROJECT/snakemake-example/trimmed/H667-1_R1_trimmed.fastq
/project/ateeq/PROJECT/snakemake-example/trimmed/H667-1_R2_trimmed.fastq
/project/ateeq/PROJECT/snakemake-example/report/H667-1.html
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
尽管我将等待时间增加了2000秒,但仍然会引发错误
snakemake -s snakefile -j 30 --latency-wait 2000
我正在使用snakemake版本5.4.5和Python 3.6.8。请让我知道我要去哪里错了,这将对我有很大的帮助
感谢您的帮助
此致
戴夫
答案 0 :(得分:1)
我不知道这是否是由于复制粘贴导致的,但缩进是错误的:
rule trimming:
input: fwd="/project/ateeq/PROJECT/snakemake-example/raw_data/{smp}_R1.fastq.gz",rev="/project/ateeq/PROJECT/snakemake-example/raw_data/{smp}_R2.fastq.gz"
output: fwd="/project/ateeq/PROJECT/snakemake-example/trimmed/{smp}_R1_trimmed.fastq", rev="/project/ateeq/PROJECT/snakemake-example/trimmed/{smp}_R2_trimmed.fastq", rep="/project/ateeq/PROJECT/snakemake-example/report/{smp}.html"
threads: 30
message: """--- Trimming."""
shell: """
fastp -i {input.fwd} -I {input.rev} -o {output.fwd} -O {output.rev} --detect_adapter_for_pe --disable_length_filtering --correction --qualified_quality_phred 30 --thread 16 --html {output.rep} --report_title "Fastq Quality Control Report" &>>{input.fwd}.log
"""
应该不是:
rule trimming:
input:
fwd="/project/ateeq/PROJECT/snakemake-example/raw_data/{smp}_R1.fastq.gz",
rev="/project/ateeq/PROJECT/snakemake-example/raw_data/{smp}_R2.fastq.gz"
output:
fwd="/project/ateeq/PROJECT/snakemake-example/trimmed/{smp}_R1_trimmed.fastq",
rev="/project/ateeq/PROJECT/snakemake-example/trimmed/{smp}_R2_trimmed.fastq",
rep="/project/ateeq/PROJECT/snakemake-example/report/{smp}.html"
threads: 30
message: """--- Trimming."""
shell: """
fastp -i {input.fwd} -I {input.rev} -o {output.fwd} -O {output.rev} --detect_adapter_for_pe --disable_length_filtering --correction --qualified_quality_phred 30 --thread 16 --html {output.rep} --report_title "Fastq Quality Control Report" &>>{input.fwd}.log
"""