如何解决尝试使用示例组信息遇到关于模块“纸浆”的 AttributeError
蛇形版本
5.25.0
描述错误
我正在尝试按组 merge
-like operation 构建规则。试运行没问题,但 snakemake -p -j1
因此错误而失败
AttributeError: module 'pulp' has no attribute 'apis'
日志
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
2 IDRPeakMerge
1 all
3
Traceback (most recent call last):
File ".../miniconda3/lib/python3.7/site-packages/snakemake/__init__.py",line 735,in snakemake
keepincomplete=keep_incomplete,File ".../miniconda3/lib/python3.7/site-packages/snakemake/workflow.py",line 972,in execute
success = scheduler.schedule()
File ".../miniconda3/lib/python3.7/site-packages/snakemake/scheduler.py",line 406,in schedule
else self.job_selector_ilp(needrun)
File ".../miniconda3/lib/python3.7/site-packages/snakemake/scheduler.py",line 616,in job_selector_ilp
if pulp.apis.LpSolverDefault is None:
AttributeError: module 'pulp' has no attribute 'apis'
最小示例
SAMPLES = {
'group1':["SRR1552451","SRR1552453","ERR127302"],'group2':["ERR127302","SRR1552452"]
}
rule all:
input:
expand('idr/{group}.idr.peak',group=list(SAMPLES.keys()))
rule IDRPeakMerge:
input:
lambda wildcards: expand('macs2/{sample}.summits.bed',sample=SAMPLES[wildcards.group])
output:
'idr/{group}.idr.peak'
run:
shell("head -n 1 {input} >> {output} ")
其他背景 文件树
s03peaks
├── idr
└── macs2
├── ERR127302.summits.bed
├── SRR1552451.summits.bed
├── SRR1552452.summits.bed
└── SRR1552453.summits.bed
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