如果指定了--drmaa-log-dir，则snakemake作业将失败

Question

我使用的是snakemake v5.7.0。无论是在本地启动还是通过snakemake --drmaa提交到SLURM，管道都能正常运行:提交作业后，一切都按预期运行。但是，在后一种情况下，会在当前目录中生成多个slurm日志文件。

使用--drmaa-log-dir选项调用的Snakemake将创建选项中指定的目录，但无法执行规则。不会生成日志文件。

下面是一个最小的例子。首先，使用Snakefile：

rule all:
  shell: "sleep 20 & echo SUCCESS!"

下面是snakemake --drmaa的输出

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

[Fri Apr 10 21:03:50 2020]
rule all:
    jobid: 0

Submitted DRMAA job 0 with external jobid 13321.
[Fri Apr 10 21:04:00 2020]
Finished job 0.
1 of 1 steps (100%) done
Complete log: /XXXXX/snakemake_test/.snakemake/log/2020-04-10T210349.984931.snakemake.log

下面是snakemake --drmaa --drmaa-log-dir foobar的输出

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

[Fri Apr 10 21:06:19 2020]
rule all:
    jobid: 0

Submitted DRMAA job 0 with external jobid 13322.
[Fri Apr 10 21:06:29 2020]
Error in rule all:
    jobid: 0
    shell:
        sleep 20 & echo SUCCESS!
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Error executing rule all on cluster (jobid: 0, external: 13322, jobscript: /XXXXXX/snakemake_test/.snakemake/tmp.9l7fqvgg/snakejob.all.0.sh). For error details see the cluster log and the log files of the involved rule(s).
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /XXXXX/snakemake_test/.snakemake/log/2020-04-10T210619.598354.snakemake.log

不会生成日志文件。目录foobar已创建，但为空。

我做错了什么？

Answer 1

在slurm中使用--drmaa-log-dir的问题是reported before，但不幸的是到目前为止还没有已知的解决方案。