RepeatModeler to identify repeats de novo in some genomic sequences. However, I'm running into an error I don't quite understand. Here is the last bit of the terminal output.
100% completed, 0:0:0 (hh:mm:ss) est. time remaining. - Comparing batch-(85 of 86) to database: Converted 1 GIs 100% completed, 0:0:0 (hh:mm:ss) est. time remaining. Comparison Time: 0:8:7 Elapsed Time, 26954 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 ).. RECON Elapsed: 0:0:1 Elapsed Time - RECON: Running re-definition of edges ( edgeredef ).. edgeredef failed. Exit code 768 Command exited with non-zero status 2 1489.43user 3.94system 12:16.75elapsed 202%CPU (0avgtext+0avgdata 1461360maxresident)k 0inputs+135472outputs (0major+2254814minor)pagefaults 0swaps
It looks like RepeatModeler is failing shortly after it calls RECON, which in turn calls a few programs itself.. I've never used RECON before and I'm not sure what the
edgeredef program does, but it is failing. RECON successfully calls some other programs that seem to work fine, so I don't really know what the problem could be. Any ideas?
By the way, these are the commands I used to run
$ BuildDatabase -name 79BACs.fas 79BACs.fas $ nohup time RepeatModeler -database 79BACs.fas > out.txt 2>&1 &
The exit code 768 doesn't seem to correspond to anything known. Couldn't it be a problem of memory? By the way, a couple of years ago, I developed TEdenovo, a de novo pipeline to identify TEs in genomic sequences, part of the REPET package (http://urgi.versailles.inra.fr/Tools/REPET). It also uses RECON. I compared TEdenovo extensively with RepeatModeler and other programs, you may find it interesting (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016526).
REPET is not easy to use and configure
I got the same error
Does anyone know how do deal with it?
I have the same problem, did you manage to solve this? Thanks
I am also getting the same error. Has this already been fixed? Please let me know the solution.
Same error, any ideas?
What is the reason for the error?
Sorry to bump such an old thread, but I have the same issue.
I'm running RECON as a standalone. I've got the same exit code from both versions of RECON (1.05 and 1.08).
This is my command:
And this is the error I get:
As I said, sorry to bump an old thread but there are not many places online where several people who have experienced this error are already gathered in place.
Did you manage to fix it? Because now I have the same error
Hi @tuentje.peeters - so sorry for not seeing this before. No, I did not, I think I moved on to do something else. It looks like @WDbakker, below, has succeeded in getting around the problem.
Encountered the same problem: RepeatModeler version 2.0. Anyone able to fix it?