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Old 03-01-2015, 04:39 PM   #1
fahmida
Member
 
Location: Australia

Join Date: Aug 2010
Posts: 54
Default 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.
fahmida is offline   Reply With Quote
Old 07-21-2015, 09:41 AM   #2
milo0615
Member
 
Location: Walnut, California

Join Date: Dec 2012
Posts: 39
Default
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
Quote:
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.
milo0615 is offline   Reply With Quote
Old 08-12-2015, 05:50 PM   #3
fahmida
Member
 
Location: Australia

Join Date: Aug 2010
Posts: 54
Default
I think the issue was with previous versions of RECON.
Current updated version (v1.08) as described in:
http://www.repeatmasker.org/RepeatModeler.html
and is available in:
http://www.repeatmasker.org/RECON-1.08.tar.gz
This one works fine for me and I no longer see the error.

Quote:
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
fahmida is offline   Reply With Quote
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