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  • Can use multiple CPUs or thread to speed up the running rate for tofu_wrap.py?

    Hi, there. I have 7 smrtcell data. It's really slow to run tofu_wrap.py, I want to know to weather I can use multiple CPUs or thread to speed up the running rate. Thank you for any tips!

  • #2
    Hi,

    Short answer is yes. There are multiple ways to hack tofu_wrap.py -- will require additional monitoring of the parallel jobs. But I first need to ask what parameters did you use to call tofu_wrap.py? What are the size bins (aka what are the subdirectories in clusterOut/)? Do you have an SGE cluster? Do you have multiple nodes from which you can run parallel pbtranscript.py cluster jobs?

    Also, please consider joining the Iso-Seq google group: https://groups.google.com/forum/#!forum/smrt_isoseq

    Since tofu_wrap.py is on the cutting edge (it's not officially supported in SMRTAnalysis 2.x but is on the agenda for SMRTAnalysis 3.x), the google group is better suited

    --Liz

    Comment


    • #3
      Originally posted by Magdoll View Post
      Hi,

      Short answer is yes. There are multiple ways to hack tofu_wrap.py -- will require additional monitoring of the parallel jobs. But I first need to ask what parameters did you use to call tofu_wrap.py? What are the size bins (aka what are the subdirectories in clusterOut/)? Do you have an SGE cluster? Do you have multiple nodes from which you can run parallel pbtranscript.py cluster jobs?

      Also, please consider joining the Iso-Seq google group: https://groups.google.com/forum/#!forum/smrt_isoseq

      Since tofu_wrap.py is on the cutting edge (it's not officially supported in SMRTAnalysis 2.x but is on the agenda for SMRTAnalysis 3.x), the google group is better suited

      --Liz
      Code:
      tofu_wrap.py --nfl_fa isoseq_nfl.fasta --ccs_fofn reads_of_insert.fofn --bas_fofn input.fofn -d clusterOut --quiver --bin_manual "(0,2,4,6,8,9,10,11,12,13,15,17,19,20,23)" --gmap_db /zs32/data-analysis/liucy_group/llhuang/Reflib/gmapdb --gmap_name gmapdb_h19 --output_seqid_prefix human isoseq_flnc.fasta final.consensus.fa
      The lab's sever is high-powered single-node computer and
      has no an SGE cluster. Can I use multiple CPUs to run command?

      Comment


      • #4
        Without SGE, it will be slow anyway.

        But if you think that single node can handle it, one way is to run multiple instances of `pbtranscript.py cluster` on the different bins.

        ex: tofu_wrap.py always creates bins 0to1kb_part0, 1to2kb_part0, etc

        You can terminate tofu_wrap and keep the bins as they are. Then separately in each bin call a separate instance of cluster:

        pbtranscript.py cluster isoseq_flnc.fasta final.consensus.fa \
        --nfl_fa isoseq_nfl.fasta -d cluster --ccs_fofn reads_of_insert.fofn \
        --bas_fofn input.fofn --quiver --use_sge \
        --max_sge_jobs 40 --unique_id 300 --blasr_nproc 24 --quiver_nproc 8

        (for you, you would remove the --use_sge and --max_sge_jobs option)

        (see cluster tutorial here: https://github.com/PacificBioscience...-and-Quiver%29)

        My guess is this would make it a bit faster but still relatively slow since everything is running in serial instead of parallel, but may be better than nothing...

        Comment

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