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  • Pacbio assemble with mira4

    Trying to assemble a bacteria genome with MIRA4, using reads from Pacbio and IonTor.
    But the reads didn't pass the basicDataChecks: the pacbio reads too long?

    "
    Read m141209_070254_42203_c100678342550000001823141002221583_s1_p0/119779/0_44266 has 44266 bases (clipped). Too long (>29990)
    Read m141209_070254_42203_c100678342550000001823141002221583_s1_p0/136033/11478_42425 has 30947 bases (clipped). Too long (>29990)
    Read m141209_070254_42203_c100678342550000001823141002221583_s1_p0/161384/0_37936 has 37936 bases (clipped). Too long (>29990)
    Read m141209_112207_42203_c100678342550000001823141002221584_s1_p0/56253/0_36182 has 36182 bases (clipped). Too long (>29990)
    Read m141209_112207_42203_c100678342550000001823141002221584_s1_p0/69528/4779_34853 has 30074 bases (clipped). Too long (>29990)
    Read m141209_112207_42203_c100678342550000001823141002221584_s1_p0/5071/17719_51457 has 33738 bases (clipped). Too long (>29990)
    Read m141209_112207_42203_c100678342550000001823141002221584_s1_p0/6435/6862_39060 has 32198 bases (clipped). Too long (>29990)
    Read m141209_112207_42203_c100678342550000001823141002221584_s1_p0/19012/11491_47096 has 35605 bases (clipped). Too long (>29990)
    Read m141209_112207_42203_c100678342550000001823141002221584_s1_p0/19963/1743_40146 has 38403 bases (clipped). Too long (>29990)
    Read m141209_112207_42203_c100678342550000001823141002221584_s1_p0/30901/8942_41549 has 32607 bases (clipped). Too long (>29990)
    More long reads may exist, but stopping output here.

    ...

    Fatal error (may be due to problems of the input data or parameters):

    ********************************************************************************
    * MIRA found 22 very long reads (too long for normal reads), see log above. *
    ********************************************************************************
    ->Thrown: void Assembly::basicDataChecks()
    ->Caught: main
    "

    I also attached the manifest file and the logfile.
    Is there a parameter that I can ignore the warning? So i can make mira running? Thanks!
    Attached Files

  • #2
    Any particular reason why you are using Mira over PBcR (Celera Assembler) which is much more well established for assembling PacBio data?

    Comment


    • #3
      Which version of MIRA exactly? Have you asked on the mira_talk mailing list?

      Comment


      • #4
        Originally posted by maubp View Post
        Which version of MIRA exactly? Have you asked on the mira_talk mailing list?
        I'm using Mira 4.0.
        No, I haven't ask the mira talk yet.

        Comment


        • #5
          Originally posted by rhall View Post
          Any particular reason why you are using Mira over PBcR (Celera Assembler) which is much more well established for assembling PacBio data?
          Have Mira 4.0 already installed. And plan hybrid assemble with IonT data.
          But I will check the CA now. Thanks!

          Comment


          • #6
            MIRA 4.0 is already out of date, the current stable version is MIRA 4.0.2
            MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and…


            There is also a newer development series available as well, MIRA 4.9.x (essentially what will become MIRA v5 once Bastien is happy with it).

            I don't know if any specific PacBio fixes have been included since MIRA 4.0 was released.
            Last edited by maubp; 12-30-2014, 02:54 AM. Reason: typo

            Comment

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