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  • CD-HIT: Sequence clustering software - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1191 ] CD-HIT-EST requires a negative amount of memory
    Date:
    04/14/14 08:10
    Submitted by:
    jereminator56
    Assigned to:
    unset
    Category:
    Clustering
    Priority:
    5
    Ticket group:
    Critical
    Resolution:
    Unset
    Summary:
    CD-HIT-EST requires a negative amount of memory
    Original submission:
    When running CD-HIT-EST through the tr2aacds.pl pipeline (http://arthropods.eugenes.org/genes2/about/EvidentialGene_trassembly_pipe.html), it returns the following error message in a log file :

    ================================================================
    Program: CD-HIT, V4.5.4 (+OpenMP), Apr 11 2014, 11:06:45
    Command: /module/apps/cd-hit/4.5.4/cd-hit-est -c 1.00 -M 1000
    -l 89 -d 0 -i ./Trinity-SOAP-TAnr.cds -o
    ./Trinity-SOAP-TAnrcd1.cds

    Started: Fri Apr 11 12:25:06 2014
    ================================================================
    Output
    ----------------------------------------------------------------
    total seq: 1631766
    longest and shortest : 50232 and 90
    Total letters: 384949449
    Sequences have been sorted

    Fatal Error:
    not enough memory, please set -M option greater than -140463122

    Program halted !!


    Approximated minimal memory consumption:
    Sequence : 590M
    Buffer : 1 X -140463832M = -140463832M
    Table : 1 X 42M = 42M
    Miscellaneous : 26M
    Total : -140463172M

    Even when giving a lot of memory to cd-hit-est through the -M option, this error occurs and it seems that the buffer requires a negative amount of memory...
    I have read on an other bug report that memory consumption errors could be caused by a bad compilation ; e.g : a 32-bit installation on a 64-bit platform... However the installation does not give the choice between 32 and 64 bit.

    Thank you for the time you may accept to spend on this issue.
    Please log in to add comments and receive followups via email.
    Followups
    Comment Date By
    There is a newer version than the 4.5.4. It is available on the Google Code link but not on the Bioinformatics.org link from the official cd-hit page (http://weizhong-lab.ucsd.edu/cd-hit/download.php).

    Installing this 4.6.1 version solves this problem.

    Bug may now be closed.
    04/18/14 07:47 jereminator56
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