Nextflow Units file specified is not found. Please provide a valid file.

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英文:

Nextflow Units file specified is not found. Please provide a valid file

问题

以下是您提供的内容的翻译：

  1. 我有以下的 Nextflow 脚本，它在下面提到的目录中运行工具 perf，对所有分割的 fastq 文件进行处理。当我运行脚本时，我收到以下错误：
  3.     * 执行进程时发生错误 > 'perf (29)'
  4.      原因是:
  5.      进程 'perf (29)' 以错误的退出状态 (1) 终止
  6.      执行的命令:
  7.      /proj/perf/bin/PERF -i Condition_R1paired.part_016.fastq -o Condition_R1paired.part_016.tsv --格式 fastq -m 1 -M 6 -u repeat_units.txt
  8.      命令退出状态:
  9.       1
  10.      命令输出:
  11.      (空)
  12.      命令错误:
  13.      指定的单位文件不存在。请提供有效的文件
  14.      工作目录:
  15.      /proj/perf/work/57/c9208b00b8c5c82c3f1fdf6c7d0f07
  16.     *提示: 通过切换到进程工作目录并显示名为 `.command.sh` 的脚本文件，您可以尝试找出问题在哪里**
  18. 这是脚本
  20.     params.fastq_dir = "/proj/split_fastq/*.fastq";
  22.     params.outdir = '/proj/work/output';
  24.     fastq_file_index=Channel.fromPath(params.fastq_dir, checkIfExists: true ).map { it -> [it.baseName, it] }
  26.     process perf {
  27.    
  28.     publishDir("${params.outdir}", mode: 'copy')
  29.    
  30.     输入:
  31. 	tuple val(file_name), path(fastq_file)
  32.     
  33.     输出:
  34.     path "${file_name}.tsv"
  35.    
  36.     
  37.     脚本:
  38.     """
  39.     /proj/perf/bin/PERF -i ${fastq_file} -o ${file_name}.tsv --格式 fastq -m 1 -M 6 -u repeat_units.txt
  41.     """
  42.   
  43.      }
  46.     工作流程 {
  47.    
  48.         perf(fastq_file_index).view()
  49.    
  50.      }
  52. 对于疑似错误和潜在修复的任何提示都欢迎，我猜测 repeat_units.txt 无法与所有 Nextflow 进程同时共享？如果是这样，如何将一个文件与多个进程共享？此外，欢迎提供改进代码的任何指针，因为我是 Nextflow 的新手。谢谢

希望这有助于您理解您的脚本和错误信息。如果您需要进一步的帮助，请随时提问。

英文:

I have a following nextflow script which runs a tool perf on all the split fastq files located in the below mentioned directory. When I run the script I get the following error:

  1. *Error executing process > 'perf (29)'
  2.  Caused by:
  3.  Process `perf (29)` terminated with an error exit status (1)
  4.  Command executed:
  5.  /proj/perf/bin/PERF -i Condition_R1paired.part_016.fastq -o Condition_R1paired.part_016.tsv --format fastq -m 1 -M 6 -u repeat_units.txt
  6.  Command exit status:
  7.   1
  8.  Command output:
  9.  (empty)
  10.  Command error:
  11.  Units file specified is not found. Please provide a valid file
  12.  Work dir:
  13.  /proj/perf/work/57/c9208b00b8c5c82c3f1fdf6c7d0f07
  14. *Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script* file named `.command.sh`**

This is the script

  1. params.fastq_dir = "/proj/split_fastq/*.fastq"
  3. params.outdir = '/proj/work/output'
  5. fastq_file_index=Channel.fromPath(params.fastq_dir, checkIfExists: true ).map { it -> [it.baseName, it] }
  7. process perf {
  9. publishDir("${params.outdir}", mode: 'copy')
  11. input:
  12. tuple val(file_name), path(fastq_file)
  14. output:
  15. path "${file_name}.tsv"
  18. script:
  19. """
  20. /proj/perf/bin/PERF -i ${fastq_file} -o ${file_name}.tsv --format fastq -m 1 -M 6 -u repeat_units.txt
  22. """
  24.  }
  27. workflow {
  29.     perf(fastq_file_index).view()
  31.  }

Any tip on suspected error and potential fix is welcome, I am guessing the repeat_units.txt cannot be shared concurrently with all the nextflow processes? In that case how do I share a file with multiple processes? Also any pointers on improving the code is welcome as I am new to nextflow. Thanks

答案1

得分: 1

这实际上不是一个Nextflow错误。PERF 只是要求您提供一个单位文件：

未找到指定的单位文件。请提供一个有效的文件

一种方法是使用额外的参数来指定文件。然后，可以使用value通道将该文件传递给每个进程。请注意，当使用一个简单的值来调用进程时，该值通道会被隐式创建<sup>1</sup>。您可以尝试以下方法：

  1. params.repeat_units = '/path/to/repeat_units.txt'
  3. params.outdir = './results'
  2.     publishDir "${params.outdir}/perf", mode: 'copy'
  4.     input:
  5.     tuple val(sample_name), path(fastq_file)
  6.     path repeat_units
  8.     output:
  9.     tuple val(sample_name), path("${sample_name}.tsv")
  11.     """
  12.     PERF \\
  13.         -i "${fastq_file}" \\
  14.         -o "${sample_name}.tsv" \\
  15.         --format fastq \\
  16.         -m 1 \\
  17.         -M 6 \\
  18.         -u "${repeat_units}"
  19.     """
  20. }
  2.     Channel
  3.         .fromPath( params.fastq_files, checkIfExists: true )
  4.         .map { tuple( it.baseName, it ) }
  5.         .set { fastq_files }
  7.     repeat_units = file( params.repeat_units )
  9.     perf( fastq_files, repeat_units )
  10.  }
英文:

This is not a Nextflow error per se. PERF is just asking you to provide a units file:

> Units file specified is not found. Please provide a valid file

One way would be to use an extra parameter to specify the file. The file could then be passed to each of the processes using a value channel. Note that a value channel is implicitly created by a process when it is invoked with a simple value<sup>1</sup>. You could try the following:

  1. params.fastq_files = &quot;/proj/split_fastq/*.fastq&quot;
  2. params.repeat_units = &#39;/path/to/repeat_units.txt&#39;
  4. params.outdir = &#39;./results&#39;
  1. process perf {
  3.     publishDir &quot;${params.outdir}/perf&quot;, mode: &#39;copy&#39;
  5.     input:
  6.     tuple val(sample_name), path(fastq_file)
  7.     path repeat_units
  9.     output:
  10.     tuple val(sample_name), path(&quot;${sample_name}.tsv&quot;)
  12.     &quot;&quot;&quot;
  13.     PERF \\
  14.         -i &quot;${fastq_file}&quot; \\
  15.         -o &quot;${sample_name}.tsv&quot; \\
  16.         --format fastq \\
  17.         -m 1 \\
  18.         -M 6 \\
  19.         -u &quot;${repeat_units}&quot;
  20.     &quot;&quot;&quot;
  22. }
  1. workflow {
  3.     Channel
  4.         .fromPath( params.fastq_files, checkIfExists: true )
  5.         .map { tuple( it.baseName, it ) }
  6.         .set { fastq_files }
  8.     repeat_units = file( params.repeat_units )
  10.     perf( fastq_files, repeat_units )
  11.  }

huangapple
  • 本文由 发表于 2023年3月7日 05:16:30
  • 转载请务必保留本文链接：https://go.coder-hub.com/75655927.html
  • bioinformatics
  • fastq
  • nextflow
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