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Using lastz (FAILURE: in load_fasta_sequence)

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  • dan
    replied
    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.

    Leave a comment:


  • Hyunmin
    replied
    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!

    Leave a comment:


  • Bob-Harris
    replied
    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)

    Leave a comment:


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

    Leave a comment:


  • Hyunmin
    started a topic Using lastz (FAILURE: in load_fasta_sequence)

    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,
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