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Repeat Modeler keeps failing

I really hope someone can help me with this. I've been trying to run repeatmodeler on my denovo assembled human cell line genome. It ran for ~ 11 days then failed. It ran RepeatModeler to round #5. The following is part of the log before it failed:

RepeatModeler Round # 5
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 81000000 bp
 -- Running TRFMask on the sequence...
 -- Sample Stats:
       Sample Size 81039572 bp
       Num Contigs Represented = 1689
       Non ambiguous bp:
             Initial: 81039572 bp
             After Masking: 81039572 bp
             Masked: 0.00 % 
 -- Input Database Coverage: 120076855 bp out of 4340197656 bp ( 2.77 % )
Sampling Time: 00:05:39 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
        0% completed,  03:25:18 (hh:mm:ss) est. time remaining.
        0% completed,  33:58:57 (hh:mm:ss) est. time remaining.
        0% completed,  24:43:09 (hh:mm:ss) est. time remaining.
        0% completed,  32:55:13 (hh:mm:ss) est. time remaining.      
       :
       :
        100% completed,  00:0:00 (hh:mm:ss) est. time remaining.
Comparison Time: 07:33:34 (hh:mm:ss) Elapsed Time, 794926613 HSPs Collected
  - RECON: Running imagespread..
RECON Elapsed: 00:26:24 (hh:mm:ss) Elapsed Time
  - RECON: Running initial definition of elements ( eledef )..
RECON Elapsed: 101:13:35 (hh:mm:ss) Elapsed Time
  - RECON: Running re-definition of elements ( eleredef )..
eleredef failed. Exit code 9

Thank you in advance for your help

repeatmodeler recon eleredef
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written by olechnwin • olechnwin

1 answer

I'm leaving this here, it maybe useful for someone.

I was able to fix the error above by re-installing and re-configuring RepeatModeler. Which includes re-installing and re-configuring RepeatMasker. Most importantly I think I did not configure the RepeatMasker library correctly.

This is the log on the same Round #5 from a job that ran to completion:

RepeatModeler Round # 5
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 81000000 bp
 -- Running TRFMask on the sequence...
       10725 Tandem Repeats Masked
 -- Masking repeats from the previous rounds...
  - Masking 1 - 5 of 2080
  - Masking 16 - 30 of 2080
  - Masking 41 - 65 of 2080
  - Masking 76 - 110 of 2080
  - Masking 121 - 165 of 2080
  - Masking 176 - 230 of 2080
  - Masking 241 - 305 of 2080
  - Masking 316 - 390 of 2080
  - Masking 401 - 485 of 2080
  - Masking 496 - 590 of 2080
  - Masking 596 - 695 of 2080
  - Masking 696 - 795 of 2080
  - Masking 796 - 895 of 2080
  - Masking 896 - 995 of 2080
  - Masking 996 - 1095 of 2080
  - Masking 1096 - 1195 of 2080
  - Masking 1196 - 1295 of 2080
  - Masking 1296 - 1395 of 2080
  - Masking 1396 - 1495 of 2080
  - Masking 1496 - 1595 of 2080
  - Masking 1596 - 1695 of 2080
  - Masking 1696 - 1795 of 2080
  - Masking 1796 - 1895 of 2080
  - Masking 1896 - 1995 of 2080
  - Masking 1996 - 2080 of 2080
 -- Sample Stats:
       Sample Size 81015363 bp
       Num Contigs Represented = 1163
       Non ambiguous bp:
             Initial: 81015363 bp
             After Masking: 50590492 bp
             Masked: 37.55 % 
 -- Input Database Coverage: 120079043 bp out of 2789776725 bp ( 4.30 % )
Sampling Time: 00:59:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
        0% completed,  11:15:40 (hh:mm:ss) est. time remaining.
        0% completed,  10:40:52 (hh:mm:ss) est. time remaining.
        0% completed,  10:11:21 (hh:mm:ss) est. time remaining.
        :

Notice how the above log have Masked: 37.55 % instead of 0% in previous log, also it actually masked something.

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written by olechnwin • olechnwin

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