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--immediate-submit当我使用and提交作业时--dependency=afterok:{dependencies}，临时文件甚至在依赖临时文件的规则启动之前就被删除了。以正常方式运行时，它工作得很好。有没有其他人遇到过这个问题？

Snakemake 脚本

rule all:
    input: 'file2', 'file3'

rule one:
    input: 'file1'
    output: temp('file2')
    shell: "touch {output}"

rule two:
    input: 'file2'
    output: 'file3'
    shell: "touch {output}"

提交命令

snakemake -s sample.snake --cluster '../mybatch.py {dependencies}' -j 4 --immediate-submit

Snakemake 输出消息

Provided cluster nodes: 4
Job counts:
        count   jobs
        1       all
        1       one
        1       two
        3

rule one:
    input: file1
    output: file2
    jobid: 1


rule two:
    input: file2
    output: file3
    jobid: 2


localrule all:
    input: file2, file3
    jobid: 0

Removing temporary output file file2.
Finished job 0.
1 of 3 steps (33%) done

Removing temporary output file file2.
Finished job 1.
2 of 3 steps (67%) done

localrule all:
    input: file2, file3
    jobid: 0

Removing temporary output file file2.
Finished job 0.
3 of 3 steps (100%) done
Error in job two while creating output file file3.
ClusterJobException in line 9 of /faststorage/home/veera/pipelines/ipsych-GATK/test/sample.snake:
Error executing rule two on cluster (jobid: 2, jobscript: /faststorage/home/veera/pipelines/ipsych-GATK/test/.snakemake/tmp.cmvmr3lz/snakejob.two.2.sh). For
detailed error see the cluster log.
Will exit after finishing currently running jobs.

错误信息

Missing files after 5 seconds:
file2
/faststorage/home/veera/pipelines/ipsych-GATK/test/.snakemake/tmp.jqh2qz0n
touch: cannot touch `/faststorage/home/veera/pipelines/ipsych-GATK/test/.snakemake/tmp.jqh2qz0n/1.jobfailed': No such file or directory
Missing files after 5 seconds:
file2

作业正在以适当的依赖关系提交。../mybatch.py​​ 是 sbatch 的自定义包装脚本。这是我的代码中的错误还是错误？我在这里先向您的帮助表示感谢。

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0 回答 0