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Using lastz (FAILURE: in load_fasta_sequence)

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  • Using lastz (FAILURE: in load_fasta_sequence)

    This is my lastz command
    $ lastz hg19/chrAll.fa[multiple] merged.fsa

    Error
    FAILURE: in load_fasta_sequence for hg19/chrAll.fa, sequence length 2,084,766,314+115,169,878 exceeds maximum (2,147,483,637)

    I got the error in above.

    What's wrong thing?

    Thanks,

  • #2
    Have you tried to do the comparison choosing a smaller set of chromosomes from hg19 at a time and checking if that works?

    Comment


    • #3
      Originally posted by Hyunmin View Post
      This is my lastz command
      $ lastz hg19/chrAll.fa[multiple] merged.fsa
      FAILURE: in load_fasta_sequence for hg19/chrAll.fa, sequence length 2,084,766,314+115,169,878 exceeds maximum (2,147,483,637)
      The short answer is you need to use lastz_32 instead of lastz.

      The long answer… the default lastz build can only handle a target up to 2Gbp combined length. This was a conscious design choice (circa 2004), as there is some efficiency gain from limiting the variables that track sequence positions to 31 bits. The lastz_32 build relaxes that constraint so that it can handle a target up to 4Gbp combined length.

      The efficiency gain was more important on machines 10 years ago than it is now, but for backward compatibility I am keeping that as the default behavior. I'll (probably) change this error report on future releases so that it tells the user to consider using lastz_32.

      The issue is discussed in the readme file here:
      http://www.bx.psu.edu/~rsharris/last...v_whole_genome

      Bob H
      (lastz author)

      Comment


      • #4
        Originally posted by Bob-Harris View Post
        The short answer is you need to use lastz_32 instead of lastz.

        The long answer… the default lastz build can only handle a target up to 2Gbp combined length. This was a conscious design choice (circa 2004), as there is some efficiency gain from limiting the variables that track sequence positions to 31 bits. The lastz_32 build relaxes that constraint so that it can handle a target up to 4Gbp combined length.

        The efficiency gain was more important on machines 10 years ago than it is now, but for backward compatibility I am keeping that as the default behavior. I'll (probably) change this error report on future releases so that it tells the user to consider using lastz_32.

        The issue is discussed in the readme file here:
        http://www.bx.psu.edu/~rsharris/last...v_whole_genome

        Bob H
        (lastz author)
        sorry, my late thread..

        I solve the problem with upper.
        Thanks!

        Comment


        • #5
          I'm trying lastz-1.03.73 from here: http://www.bx.psu.edu/~rsharris/lastz/newer/

          But I don't see lastz_32... Is this now the default behaviour?

          I just tried 'make lastz_32' and it appeared :-D


          Thanks,
          Last edited by dan; 07-21-2016, 06:20 AM.
          Homepage: Dan Bolser
          MetaBase the database of biological databases.

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