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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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Edge redefinition errror #255

Open culot007 opened 2 months ago

culot007 commented 2 months ago

Hello,

I am having approximately the same issue as here, but I cannot figure out how JennyHTLee resolved their problem. Any help would be appreciated!

# Last lines of log file
     100% completed,  00:0:00 (hh:mm:ss) est. time remaining.
Comparison Time: 01:16:00 (hh:mm:ss) Elapsed Time, 332778 HSPs Collected
  - RECON: Running imagespread..
RECON Elapsed: 00:00:01 (hh:mm:ss) Elapsed Time
  - RECON: Running initial definition of elements ( eledef )..
RECON Elapsed: 00:23:12 (hh:mm:ss) Elapsed Time
  - RECON: Running re-definition of elements ( eleredef )..
RECON Elapsed: 06:09:32 (hh:mm:ss) Elapsed Time
  - RECON: Running re-definition of edges ( edgeredef )..
edgeredef failed. Exit code 1024

# Last lines of round-5/edge_redef_res/log
evaluating definition of element 6978
new clan: 4522 for ele 6978
clan size: 389, clan core size: 12
evaluating definition of element 6979
new clan: 4523 for ele 6979
error:  more edges in file for ele 68133

Here is the round-5 directory: https://drive.google.com/file/d/1i5nPjOXP4IX9IGdq2Y4Thrn87nnhxsQq/view?usp=sharing

Versions Repeatmasker 2.0.1 RepeatMasker 4.1.1 RepeatScout 1.0.6 TRF 4.09

rmhubley commented 2 weeks ago

Thanks for sharing the round-5 data, I will download this to take a deeper look. Unfortunately problems like this are hard to fix as we have to dive into RECON a program we didn't develop and no one else supports. Luckily this type of failure is rare. Since RepeatModeler employs a sampling approach, it is often the case that rerunning on the same genome (using a new set of sequence samples) will not fall into the same bug that the previous run did. RECON is pretty stable but there is definitely a rare edge case that is not being handled correctly.