输入与输出：作业成功完成，但是缺少一些输出文件

如何解决输入与输出：作业成功完成，但是缺少一些输出文件

我认为我的管道失败了，因为预期的全部规则输出与实际最终输出之间存在冲突。我相信snakemake正在等待文件kma/{sample}没有扩展名出现，相反，它正在获取包含multiext("kma/{sample}",".res",".aln",".fsa",".gz")的目录，而我很难使它们正常播放。

configfile: "config.yaml"

rule all:
    input:
        expand("kma/{sample}",sample = config["samples"])
        #multiext("kma/{sample}",".gz",sample = config["samples"])

rule seqtk_qualtiy_filter:
    input:
        lambda wildcards: "S5_Raw/" + config["samples"][wildcards.sample]
    output:
        temp("qtrim/{sample}.qtrim.fq")
    shell:
        "seqtk trimfq -b 0.01 {input} > {output}"

rule seqtk_clip:
    input:
        "qtrim/{sample}.qtrim.fq"
    output:
        temp("clip/{sample}.clip.fq")
    shell:
        "seqtk trimfq -b20 -L 350 {input} > {output}"

rule bbnorm:
    input:
        "clip/{sample}.clip.fq"
    output:
        "S5_processed/{sample}.norm.fq"
    shell:
        "bbnorm.sh in={input} out={output} target=100"

rule kma_map:
    input:
        "S5_processed/{sample}.norm.fq"
    params:
        ref = "ref/consensus.fasta"
    output:
        directory("kma/{sample}")
        #multiext("kma/{sample}",".gz")
    shell:
        "kma -i {input} -t_db {params.ref} -o {output}"

如果您以kma希望看到处理完成的方式运行该错误，则该错误

Waiting at most 5 seconds for missing files.
MissingOutputException in line 33 of /home/sean/Desktop/reo/antisera project/ReovirusS1AmpliconS5.smk:
Job completed successfully,but some output files are missing. Missing files after 5 seconds:
kma/BA8359-19
This might be due to filesystem latency. If that is the case,consider to increase the wait time with --latency-wait.
  File "/home/sean/.local/lib/python3.6/site-packages/snakemake/executors/__init__.py",line 544,in handle_job_success
  File "/home/sean/.local/lib/python3.6/site-packages/snakemake/executors/__init__.py",line 231,in handle_job_success
Shutting down,this might take some time.

我也尝试过增加延迟时间，但是由于从未真正创建预期的文件，因此等待多长时间都没有关系。

使用multiext函数时收到的错误

Error in rule kma_map:
    jobid: 11
    output: kma/BA8359-19.res,kma/BA8359-19.aln,kma/BA8359-19.fsa,kma/BA8359-19.frag.gz
    shell:
        kma -i S5_processed/BA8359-19.norm.fq -t_db ref/consensus.fasta -o kma/BA8359-19.res kma/BA8359-19.aln kma/BA8359-19.fsa kma/BA8359-19.frag.gz
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down,this might take some time.
Exiting because a job execution failed. Look above for error message

我相信会发生此错误，因为snakemake在-o标志中列出了所有文件类型，而kma则拒绝。

解决方法

编辑21SEP2020

我已经找到了运行此应用程序的正确方法。

首先，我需要像这样的rule all

KMA_OUTPUTS = [".res",".aln",".fsa",".frag.gz"]

rule all:
    input:
        expand("kma/{sample}{ext}",sample = config["samples"],ext = KMA_OUTPUTS)

然后是kma的规则

rule kma_map:
    input:
        "S5_processed/{sample}.norm.fq"
    params:
        ref = "ref/consensus.fasta",prefix = "kma/{sample}"
    output:
        multiext("kma/{sample}",".res",".frag.gz")
    shell:
        "kma -i {input} -t_db {params.ref} -o {params.prefix}"

通过使用parama.prefix作为输出文件输入，我可以获得所需的输出。

,

规则all中的输入文件与规则kma_map中的输出文件之间可能存在不一致。显示错误信息会有所帮助。

无论如何，您似乎尝试过的命令multiext("kma/{sample}",".gz",sample = config["samples"])不应编译，因为multiext不接受命名参数。也许您想要的是这样：

rule all:
    input:
        expand("kma/{sample}{ext}",sample= config['samples'],ext= [".res",".gz"]),rule kma_map:
    ...
    output:
        multiext("kma/{sample}",".gz")
    shell:
        "kmap ... {input} {output}"