介绍

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使用

  1. LTR_FINDER_parallel -h
  2. ## 
  3. ## ~ ~ ~ Run LTR_FINDER in parallel ~ ~ ~
  4. ## 
  5. ## Author: Shujun Ou (shujun.ou.1@gmail.com)
  6. ## Date: 09/19/2018
  7. ## Update: 09/27/2019
  8. ## 
  9. ## Usage: perl LTR_FINDER_parallel -seq [file] -size [int] -threads [int]
  10. ## Options:        -seq    [file]  Specify the sequence file.
  11. ##                 -size   [int]   Specify the size you want to split the genome sequence.
  12. ##                                 Please make it large enough to avoid spliting too many LTR elements. Default 5000000 (bp)
  13. ##                 -time   [int]   Specify the maximum time to run a subregion (a thread).
  14. ##                                 This helps to skip simple repeat regions that take a substantial of time to run. Default: 1500 (seconds).
  15. ##                                 Suggestion: 300 for -size 1000000. Increase -time when -size increased.
  16. ##                 -try1   [0|1]   If a region requires more time than the specified -time (timeout), decide:
  17. ##                                         0, discard the entire region.
  18. ##                                         1, further split to 50 Kb regions to salvage LTR candidates (default);
  19. ##                 -harvest_out    Output LTRharvest format if specified. Default: output LTR_FINDER table format.
  20. ##                 -next           Only summarize the results for previous jobs without rerunning LTR_FINDER (for -v).
  21. ##                 -verbose|-v     Retain LTR_FINDER outputs for each sequence piece.
  22. ##                 -finder [file]  The path to the program LTR_FINDER (default v1.0.7, included in this package).
  23. ##                 -threads|-t     [int]   Indicate how many CPU/threads you want to run LTR_FINDER.
  24. ##                 -help|-h        Display this help information.
  • -seq: 序列文件
  • -size: 设定拆分基因组的大小
  • -time: 设定一个
  • -try1:
  • -harvest_out: 输出 LTRharvest 格式，默认输出 LTR_FINDER 表格格式。
  • -next: 不重新运行 LTR_FINDER，而仅仅是总结之前任务的运行结果。
  • -verbose, -v: 保留 LTR_FINDER 对每一个序列片段的输出。
  • -finder: LTR_FINDER 程序的路径，默认选择本程序中的 v1.0.7
  • -threads, -t: 设定线程数量。
  • -help, -h: 显示帮助信息。

运行

参考