Edgeredef Failed When Running Repeatmodeler

Question

[Daniel Standage]

I'm using 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 RepeatModeler.

$ BuildDatabase -name 79BACs.fas 79BACs.fas
$ nohup time RepeatModeler -database 79BACs.fas > out.txt 2>&1 &

[tflutre]

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).

[eennadi]

REPET is not easy to use and configure

[Buttonwood]

I got the same error

 - Comparing batch-(111 of 113) to database:
      100% completed,  0:0:0 (hh:mm:ss) est. time remaining.
 - Comparing batch-(112 of 113) to database:
      100% completed,  0:0:0 (hh:mm:ss) est. time remaining.
Comparison Time: 0:12:36 Elapsed Time, 330 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: 0:0:0 Elapsed Time
 - RECON: Running re-definition of edges ( edgeredef )..
edgeredef failed. Exit code 768

Does anyone know how do deal with it?

[jomaco]

I have the same problem, did you manage to solve this? Thanks

[Rahul Sharma]

I am also getting the same error. Has this already been fixed? Please let me know the solution.

[Alex]

Same error, any ideas?

[geruispring]

RECON: eleredef failed. Exit code 768

What is the reason for the error?

[maxwhjohn1988]

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:

perl /home/m/mwhj1/2018/programs/RECON-1.08/scripts/recon.pl a.lines.seqlist.txt \
> whole_assembly_all_v_all.msp 147878

And this is the error I get:

imagespread failed. Exit code 768

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.

[teuntje.peeters]

Did you manage to fix it? Because now I have the same error

[maxwhjohn1988]

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.

[tothepoint]

Encountered the same problem: RepeatModeler version 2.0. Anyone able to fix it?

Answer 1

[Robert Hubley]

RepeatModeler is returning the exit code of the system call. This is compound value that needs to be shifted over by 8 to get the actual return code that RECON is producing. In this case 768 >> 8 = 3. The RECON programs eleredef.c and edgeredef.c both write log files which include error messages in ele_redef_res/log and edge_redef_res/log respectively.

I have looked into this a bit and so far I have not been able to reproduce the errors being reported. If someone is still experiencing this problem and has preserved the output of the programs I would be interested in looking over the data.

Cheers,

-R

Answer 2

[WDbakker]

Just ran into the same problem using using RECON 1.0.5, exact same error message. For me compiling RECON 1.0.8 and reconfigured repeatmodeler seemed to have worked, don't get the error message again.

Answer 3

[michael.b.broe]

Exactly the same problem here. Ubuntu with 256G RAM, assigning 48 of 64 cores to run RepeatModeler on 1.6 Gbase genome.

repeatmasker 4.0.7
repeatmodeler 1.0.11
recon 1.08

all from bioconda.

Answer 4

[bioinfo17]

Encountered the same problem: RepeatModeler version open-1.0.11 RECON 1.05

> Comparison Time: 00:00:16 (hh:mm:ss) Elapsed Time, 901 HSPs Collected
>   - RECON: Running imagespread.. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time
>   - RECON: Running initial definition of elements ( eledef ).. RECON Elapsed: 00:00:01 (hh:mm:ss) Elapsed Time
>   - RECON: Running re-definition of elements ( eleredef )..

I will try compiling RECON 1.08 and reconfigure repeatmodeler as advised by WDbakker and see if this resolves.

update: this worked!! Thanks @WDbakker

Answer 5

[tothepoint]

So, Finally I got this fix. Firstly I downloaded RECON 1.08 from http://mirrors.advancedhosters.com/gentoo/distfiles/ as currently they were not providing this version for some reason.Then I configure the same outside the RepeatModeler directory and reconfigure the RepeatModeler by providing the different path for RECON.

Now it works smoothly.

Hope this will help.