Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • genometools parallel

    Hi, I am using genometools and find it quite slow with an 1G fasta file.
    When running:
    $ gt suffixerator ...
    It simply used one cpu and was quite slow. Then I tried:
    $ gt -j 4 suffixerator ...
    But nothing changed.
    So I'm really confused whether gt could use parallel processors to accelerate working, just like RepeatMasker (who has -pa to set number of parallel processors)?

  • #2
    Originally posted by hugh_hang View Post
    Hi, I am using genometools and find it quite slow with an 1G fasta file.
    When running:
    $ gt suffixerator ...
    It simply used one cpu and was quite slow. Then I tried:
    $ gt -j 4 suffixerator ...
    But nothing changed.
    So I'm really confused whether gt could use parallel processors to accelerate working, just like RepeatMasker (who has -pa to set number of parallel processors)?
    I'm curious how you decided to use the "-j" option for gt suffixerator because I have never seen that and it does not appear to be documented. Depending on what task you are trying accomplish, there are ways of running jobs in parallel but I'm not aware of any genometools applications that will use multiple processors.

    Comment


    • #3
      Originally posted by SES View Post
      I'm curious how you decided to use the "-j" option for gt suffixerator because I have never seen that and it does not appear to be documented. Depending on what task you are trying accomplish, there are ways of running jobs in parallel but I'm not aware of any genometools applications that will use multiple processors.
      I saw '-j' in LTRdigest User’s Manual where write:
      To run the protein domain search in a parallel fashion, use the -j parameter to gt to specify the number of concurrent threads to use:
      gt -j 3 ltrdigest [options] GFF3 file indexname
      I thought '-j' is an option of 'gt' command that can be added into all gt tools. Maybe I was so naive for it can only added into the command of 'gt ltrdigest'.

      Comment


      • #4
        I don't know what genometools does, but maybe it would be possible to parallelize it with gnu parallel. Have a look here to get an idea how it works..
        savetherhino.org

        Comment


        • #5
          Originally posted by rhinoceros View Post
          I don't know what genometools does, but maybe it would be possible to parallelize it with gnu parallel. Have a look here to get an idea how it works..
          It is really awesome. I know what to do next, thanks!

          Comment


          • #6
            Originally posted by hugh_hang View Post
            I saw '-j' in LTRdigest User’s Manual where write:

            I thought '-j' is an option of 'gt' command that can be added into all gt tools. Maybe I was so naive for it can only added into the command of 'gt ltrdigest'.
            LTRdigest uses HMMER for the protein domain search, so I think that "-j" option applies specifically to that routine of the LTRdigest tool.

            Comment


            • #7
              Originally posted by SES View Post
              LTRdigest uses HMMER for the protein domain search, so I think that "-j" option applies specifically to that routine of the LTRdigest tool.
              Thanks, I suddenly realized.

              Comment


              • #8
                Currently LTRdigest is the only tool to use the parallelization option -j for now, but that might change in the future.

                Comment


                • #9
                  Originally posted by sst View Post
                  Currently LTRdigest is the only tool to use the parallelization option -j for now, but that might change in the future.
                  do you know if the change will occur in the newest version in 2014?

                  Comment


                  • #10
                    Originally posted by hugh_hang View Post
                    do you know if the change will occur in the newest version in 2014?
                    Currently there are no plans multithreading the existing tools -- what I am saying is that there might be new tools using that option if they use multithreading -- sorry if my comment was misleading

                    Comment

                    Latest Articles

                    Collapse

                    • seqadmin
                      Exploring the Dynamics of the Tumor Microenvironment
                      by seqadmin




                      The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
                      07-08-2024, 03:19 PM
                    • seqadmin
                      Exploring Human Diversity Through Large-Scale Omics
                      by seqadmin


                      In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
                      06-25-2024, 06:43 AM

                    ad_right_rmr

                    Collapse

                    News

                    Collapse

                    Topics Statistics Last Post
                    Started by seqadmin, Today, 11:09 AM
                    0 responses
                    14 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 07-19-2024, 07:20 AM
                    0 responses
                    146 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 07-16-2024, 05:49 AM
                    0 responses
                    120 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 07-15-2024, 06:53 AM
                    0 responses
                    111 views
                    0 likes
                    Last Post seqadmin  
                    Working...
                    X