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  • RepeatModeler Error (eleredef failed. Exit code 768)

    Hi,

    I am stuck with RepeatModeler with error:
    eleredef failed. Exit code 768

    Here is the full log:
    HTML Code:
    /software/RepeatModeler/RepeatModeler -database test.txt -pa 10 
    RepeatModeler Version open-1.0.8
    ================================
    Search Engine = ncbi
    Database = test.txt .
      - Sequences = 2
      - Bases = 2072880
    Using output directory = /local/scratch/repeat_related/repeatmodeler/RM_16928.MonMar21132272015
    
    RepeatModeler Round # 1
    ========================
    Searching for Repeats
     -- Sampling from the database...
       - Gathering up to 40000000 bp
       - Final Sample Size = 2072880 bp ( 2020122 non ambiguous )
       - Num Contigs Represented = 2
     -- Running RepeatScout on the sequences...
       - RepeatScout: Running build_lmer_table ( l = 12 )..
       - RepeatScout: Running RepeatScout..
    Program duration is 43.0 sec = 0.7 min = 0.0 hr
    NOTE: RepeatScout did not return any models.
    
    RepeatModeler Round # 2
    ========================
    Searching for Repeats
     -- Sampling from the database...
       - Gathering up to 3000000 bp
     -- Running TRFMask on the sequence...
           144 Tandem Repeats Masked
     -- Sample Stats:
           Sample Size 2072880 bp
           Num Contigs Represented = 2
           Non ambigous bp:
                 Initial: 2020122 bp
                 After Masking: 1892786 bp
                 Masked: 6.30 % 
     -- Input Database Coverage: 2072880 bp out of 2072880 bp ( 100.00 % )
    Sampling Time: 0:0:14 Elapsed Time
    Running all-by-other comparisons...
            0% completed,  00:3:19 (hh:mm:ss) est. time remaining.
            0% completed,  00:2:22 (hh:mm:ss) est. time remaining.
            0% completed,  00:1:40 (hh:mm:ss) est. time remaining.
            0% completed,  00:1:09 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:52 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:42 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:34 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:31 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:28 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:24 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:27 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:26 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:24 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:21 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:21 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:19 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:17 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:16 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:14 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:13 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:14 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:13 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:12 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:11 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:10 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:09 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:08 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:07 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:06 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:05 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:05 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:05 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:04 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:04 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:03 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:03 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:02 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:02 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:00 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:00 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:00 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:00 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:00 (hh:mm:ss) est. time remaining.
          100% completed,  00:0:00 (hh:mm:ss) est. time remaining.
    Comparison Time: 0:0:32 Elapsed Time, 10361 HSPs Collected
      - RECON: Running imagespread..
    RECON Elapsed: 0:0:0 Elapsed Time
      - RECON: Running initial definition of elements ( eledef )..
    RECON Elapsed: 0:0:1 Elapsed Time
      - RECON: Running re-definition of elements ( eleredef )..
    eleredef failed. Exit code 768
    Anyone else encountered this problem and any potential solution?
    Thanks.

  • #2
    Hi fahmida,

    Were you able to figure out what is causing that error? I have the same problem. Please let me know.

    Thank you,

    -Milo
    Originally posted by fahmida View Post
    Hi,

    I am stuck with RepeatModeler with error:
    eleredef failed. Exit code 768

    Here is the full log:
    HTML Code:
    /software/RepeatModeler/RepeatModeler -database test.txt -pa 10 
    RepeatModeler Version open-1.0.8
    ================================
    Search Engine = ncbi
    Database = test.txt .
      - Sequences = 2
      - Bases = 2072880
    Using output directory = /local/scratch/repeat_related/repeatmodeler/RM_16928.MonMar21132272015
    
    RepeatModeler Round # 1
    ========================
    Searching for Repeats
     -- Sampling from the database...
       - Gathering up to 40000000 bp
       - Final Sample Size = 2072880 bp ( 2020122 non ambiguous )
       - Num Contigs Represented = 2
     -- Running RepeatScout on the sequences...
       - RepeatScout: Running build_lmer_table ( l = 12 )..
       - RepeatScout: Running RepeatScout..
    Program duration is 43.0 sec = 0.7 min = 0.0 hr
    NOTE: RepeatScout did not return any models.
    
    RepeatModeler Round # 2
    ========================
    Searching for Repeats
     -- Sampling from the database...
       - Gathering up to 3000000 bp
     -- Running TRFMask on the sequence...
           144 Tandem Repeats Masked
     -- Sample Stats:
           Sample Size 2072880 bp
           Num Contigs Represented = 2
           Non ambigous bp:
                 Initial: 2020122 bp
                 After Masking: 1892786 bp
                 Masked: 6.30 % 
     -- Input Database Coverage: 2072880 bp out of 2072880 bp ( 100.00 % )
    Sampling Time: 0:0:14 Elapsed Time
    Running all-by-other comparisons...
            0% completed,  00:3:19 (hh:mm:ss) est. time remaining.
            0% completed,  00:2:22 (hh:mm:ss) est. time remaining.
            0% completed,  00:1:40 (hh:mm:ss) est. time remaining.
            0% completed,  00:1:09 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:52 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:42 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:34 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:31 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:28 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:24 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:27 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:26 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:24 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:21 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:21 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:19 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:17 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:16 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:14 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:13 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:14 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:13 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:12 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:11 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:10 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:09 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:08 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:07 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:06 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:05 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:05 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:05 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:04 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:04 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:03 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:03 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:02 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:02 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:01 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:00 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:00 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:00 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:00 (hh:mm:ss) est. time remaining.
            0% completed,  00:0:00 (hh:mm:ss) est. time remaining.
          100% completed,  00:0:00 (hh:mm:ss) est. time remaining.
    Comparison Time: 0:0:32 Elapsed Time, 10361 HSPs Collected
      - RECON: Running imagespread..
    RECON Elapsed: 0:0:0 Elapsed Time
      - RECON: Running initial definition of elements ( eledef )..
    RECON Elapsed: 0:0:1 Elapsed Time
      - RECON: Running re-definition of elements ( eleredef )..
    eleredef failed. Exit code 768
    Anyone else encountered this problem and any potential solution?
    Thanks.

    Comment


    • #3
      I think the issue was with previous versions of RECON.
      Current updated version (v1.08) as described in:

      and is available in:

      This one works fine for me and I no longer see the error.

      Originally posted by milo0615 View Post
      Hi fahmida,

      Were you able to figure out what is causing that error? I have the same problem. Please let me know.

      Thank you,

      -Milo

      Comment

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