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  • Please help: In Velvetg, maximum elements addressable with 32 bits?

    Hi guys,

    I was trying to assemble a maize genome with Velvet, but got stuck here for a while. Any help is appreciated.

    some information about the machine:

    uname -a
    Linux marin 2.6.16.46-0.12-default #1 SMP Thu May 17 14:00:09 UTC 2007 ia64 ia64 ia64 GNU/Linux


    gcc -v
    Using built-in specs.
    Target: ia64-unknown-linux-gnu
    Configured with: ../gcc-4.4.0/configure --prefix=/opt/gcc/4.4.0 --with-mpfr=/opt/mpfr/2.4.1 --with-gmp=/opt/gmp/4.3.1
    Thread model: posix
    gcc version 4.4.0 (GCC)

    about the data
    pair-end fastq dataset, all in 75bp, all ~15G in *.fq.gz format



    about the binaries
    I compile the velvet source on this machine by:
    make 'OPENMP=1' 'LONGSEQUENCES=1' 'CATEGORIES=4' 'BIGASSEMBLY=1'

    and got:
    file velveth
    velveth: ELF 64-bit LSB executable, IA-64 (Intel 64 bit architecture), version 1 (SYSV), for GNU/Linux 2.6.4, dynamically linked (uses shared libs), for GNU/Linux 2.6.4, not stripped

    velvetg:
    the same.

    running and error
    velveth run through without error with the following command:
    velveth mo17 31 -reference ZmB73_RefGen_v2.RepMasked.fasta -fastq.gz -shortPaired *gz


    however, when I was trying to run velvetg with the following command, program throw out the error mentioned in the title..

    velvetg mo17/ -ins_length 500 -exp_cov auto -min_contig_lgth 100 -read_trkg yes -amos_file yes -unused_reads yes

    the error info:
    ...
    ...
    [17914.055037] Connecting 112000000 / 217984709
    [17924.646873] Connecting 57000000 / 217984709
    [17939.007915] Connecting 30000000 / 217984709
    [17939.361960] >>> Reached maximum elements addressable with 32 bits

    my trying

    I tried to recompile the source with CFLAGS= -mlp64, but got error again..

    gcc -mlp64 -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=4 -D BIGASSEMBLY -D LONGSEQUENCES -D OPENMP -c src/tightString.c -o obj/tightString.o
    cc1: error: unrecognized command line option "-mlp64"
    make: *** [obj/tightString.o] Error 1

  • #2
    Solution?

    Hi there,

    Did you ever figure out how to make this work? I'm getting the same error.

    Thanks!
    - Jason

    Comment


    • #3
      Sorry for disappointing you, I didn't make it...
      I was quite busy with other works, thus can not afford the time I might take.
      I took use of SOAPdenovo instead, and got a large number of scaffolds with gaps. It seems that the coverage is not good enough, or I just did sth stupid for the data..

      PS: I am a rather new player in the genome assembly arena

      Chen Hao

      Comment


      • #4
        Hey Chao,
        Have you found any solution? I got the same error. From the reminder, it may be caused due to run in 32bit enviroment. But I was running at state supecomputer that should be 64 bit. So strange. If you have any update, please let me know. [email protected]
        Hongtao

        Comment


        • #5
          You should post that on the velvet mailing list.

          Comment

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