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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
    04/14/14 08:10
    Submitted by:
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    CD-HIT-EST requires a negative amount of memory
    Original submission:
    When running CD-HIT-EST through the pipeline (, 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

    Started: Fri Apr 11 12:25:06 2014
    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.
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    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 link from the official cd-hit page (

    Installing this 4.6.1 version solves this problem.

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