python - Snakemake如何忽略RuntimeWarning？

Question

与默认的 Python 行为不同，Snakemake 在 numpy 抛出 RuntimeWarnings 时停止执行。

/a-path/site-packages/numpy/lib/function_base.py:3250: RuntimeWarning: All-NaN slice encountered
Exiting because a job execution failed. Look above for error message

使用下面的代码配置 numpy.seterr 没有帮助。

import numpy as np
np.seterr(all='print')

我怎样才能简单地告诉snakemake不要终止警告规则？

注意:我在 Snakemake 中使用 run: 选项作为抛出 RuntimeWarning 的规则。

Answer 1

也许您在其他地方遇到了实际错误。在 5.4.2 上，警告看起来没问题:

rule all:
    input:
        'foo.txt',

rule one:
    output:
        touch('foo.txt'),
    run:
        import numpy as np
        np.nanmax([np.nan, np.nan])

执行:

蛇形

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1   all
    1   one
    2

[Tue Jun 11 21:09:47 2019]
rule one:
    output: foo.txt
    jobid: 1

Job counts:
    count   jobs
    1   one
    1
/home/dario/miniconda3/lib/python3.6/site-packages/snakemake/workflow.py:19: RuntimeWarning: All-NaN axis encountered
  from snakemake.logging import logger, format_resources, format_resource_names
Touching output file foo.txt.
[Tue Jun 11 21:09:47 2019]
Finished job 1.
1 of 2 steps (50%) done

[Tue Jun 11 21:09:47 2019]
localrule all:
    input: foo.txt
    jobid: 0

[Tue Jun 11 21:09:47 2019]
Finished job 0.
2 of 2 steps (100%) done
Complete log: /home/dario/Tritume/.snakemake/log/2019-06-11T210947.007675.snakemake.log

在任何情况下，您都可以使用以下方法消除错误

import warnings
warnings.filterwarnings('ignore')