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  • CD-HIT-EST-2D Error: segmentation fault ('core' dumped)

    Hello,

    I am using CD-HIT-EST-2D in order to compare two contigs files in fasta format. I have been using it for several files and it worked properly until I got an error with two files. The error is: segmentation fault ('core' dumped). I give you the commands and the output:

    -----------------
    [joel@localhost results]$ /programs/cd-hit-v4.6.1-2012-08-27/./cd-hit-est-2d -i Contig_Leg_500Mb.fasta -i2 Contig_Leg_500Mb_15ntout.fasta -o Prueb.fasta -c 0.95 -n 8
    ================================================================
    Program: CD-HIT, V4.6 (+OpenMP), Feb 26 2014, 12:02:11
    Command: /programs/cd-hit-v4.6.1-2012-08-27/./cd-hit-est-2d -i
    Contig_Leg_500Mb.fasta -i2
    Contig_Leg_500Mb_15ntout.fasta -o Prueb.fasta -c 0.95
    -n 8

    Started: Mon Mar 3 12:03:48 2014
    ================================================================
    Output
    ----------------------------------------------------------------
    total seq in db1: 37276
    total seq in db2: 28500
    longest and shortest : 14632 and 201
    Total letters: 19048606
    Sequences have been sorted
    longest and shortest : 12192 and 201
    Total letters: 13606287

    Approximated minimal memory consumption:
    Sequence : 36M
    Buffer : 1 X 15M = 15M
    Table : 1 X 1M = 1M
    Miscellaneous : 0M
    Total : 54M

    Table limit with the given memory limit:
    Max number of representatives: 0
    Max number of word counting entries: 93208177

    Segmentation fault (`core' dumped)

    -----------------

    I have checked the fasta files and they look good. Besides, I have tried to use CD-HIT-EST with each file and it worked, so I don't know where is the problem. I also used CD-HIT-EST-2D for files with more and larger sequences and it worked so the problem is not with the memory limitations.
    Did someone have the same problem?

    Thanks.

  • #2
    Hi Joel 91.
    I have got the same problem. Have you fixed the issue?
    Best regards.

    Comment

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