5

以下蛇形脚本：

rule all:
    input:
        'test.done'

rule pipe:
   output:
       'test.done'
   shell:
        """
        seq 1 10000 | head > test.done
        """

失败并出现以下错误：

snakemake -s test.snake

Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1   all
    1   pipe
    2

rule pipe:
    output: test.done
    jobid: 1

Error in job pipe while creating output file test.done.
RuleException:
CalledProcessError in line 9 of /Users/db291g/Tritume/test.snake:
Command '
        seq 1 10000 | head > test.done
        ' returned non-zero exit status 141.
  File "/Users/db291g/Tritume/test.snake", line 9, in __rule_pipe
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/concurrent/futures/thread.py", line 55, in run
Removing output files of failed job pipe since they might be corrupted:
test.done
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message

解释返回非零退出状态 141似乎是说snakemake已经捕获了 SIGPIPE 发送的失败head。我想严格来说，snakemake 在捕捉失败方面做的是正确的事情，但我想知道是否有可能忽略像这样的某些类型的错误。我有一个使用该head命令的蛇形脚本，我正在尝试找到解决此错误的方法。

4

2 回答 2

6

是的，Snakemake 默认设置 pipefail，因为在大多数情况下，这是人们隐含的期望。您始终可以通过添加set +o pipefail;到 shell 命令的前面来为特定命令停用它。

于 2017-10-07T15:27:43.330 回答
2

一个笨拙的解决方案是附加|| true到脚本中。这将使命令总是干净地退出，这是不可接受的。要检查脚本是否实际成功，您可以查询数组变量${PIPESTATUS[@]}以确保它包含预期的退出代码：

这个脚本没问题：

seq 1 10000 | head | grep 1 > test.done || true
echo ${PIPESTATUS[@]}
141 0 0

这不行：

seq 1 10000 | head | FOOBAR > test.done || true
echo ${PIPESTATUS[@]}
0
于 2017-10-05T08:28:35.557 回答