即使我使用了最简单的代码结构,它也没有工作,如下所示: 规则fastqc_raw:输入:“原始/快速”输出:“输出/fastqc_raw/a.html”外壳:"fastqc {input} -o {output-t 4’返回的非零退出状态2.文件“/User/01/Desktop/Snakemake/Snakefile”,第13行,在 浏览1提问于2018-10-03得票数 3 2回答 使用Snakemake处理...
fastp -i {input.read01} -I {input.read02} -o {output.read01} -O {output.read02} --thread {threads} --html {output.html} --json {output.json} """ 这里rule all的作用还是没有搞明白,看有的文档说是最终保留的文件 ,我这里rule all 只写了了最终的html和json,但是最终的结果里是有过滤...
Building DAG of jobs... MissingInputException in line 3 of /mnt/shared/scratch/myan/private/practice_data/RNAseq/snakemake.rnaseq/gtf_list.py: Missing input files for rule all: output.gtf/['ERR188337', 'ERR188245', 'ERR188428', 'ERR188401', 'ERR204916', 'ERR188383', 'ERR...
第一行SRR后面有一个逗号 最开始没写这个逗号,一直遇到报错 Building DAG of jobs... MissingInputException in line 3 ...
我已经能够得到(我认为)比以前更远,但蛇形正在抛出一个错误,说Missing input files for rule basecall: /Users/joshl/PycharmProjects/ARS/Results/DataFiles/fast5/FAL03879_67a0761e_1055/ barcode72.fast5。我的代码相关代码在这里: 码 代码语言:javascript ...
Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards. 直译过来是:目标规则可能不包含通配符,请指定没有通配符的具体文件或规则。 看似是通配符的使用问题,实则和 rule all 的 input 错误有关。 Snakemake 的rule all 需要输入一个列表,这个列表包括所有的步骤会产生...
第二个rule就是不运行 原来是在rule all 代码里少写了 第二个rule的输出文件 正确写法是 SRR, = glob_wildcards("output.gtf/"+"{srr}.gtf") #SRR = ["ERR188401","ERR204916"] rule all: input: #expand("output.gtf/"+"{srr}.gtf",srr=SRR), ...
Missing input files for rule make_b: output: b.txt affected files: a.txt despite the fact that all I wanted to do was delete the output if it existed. If I had to guess, in the second case, snakemake is building the DAG and omitting themake_brule because an input doesn't exist. ...
rule fastp_se: input: raw/GSM6001951_L3.fastq.gz output: results/trimmed/GSM6001951_L3.fastq.gz, report/GSM6001951_L3.fastp.html, report/GSM6001951_L3.fastp.json log: logs/fastp/GSM6001951_L3.log jobid:30 reason: Missing output files: report/GSM6001951_L3.fastp.json, results/trimmed...
rule fastp_se: input: raw/GSM6001951_L3.fastq.gz output: results/trimmed/GSM6001951_L3.fastq.gz, report/GSM6001951_L3.fastp.html, report/GSM6001951_L3.fastp.json log: logs/fastp/GSM6001951_L3.log jobid: 30 reason: Missing output files: report/GSM6001951_L3.fastp.json, results/trimmed...