Question: Edgeredef Failed When Running Repeatmodeler
2
gravatar for Daniel Standage
9.6 years ago by
Daniel Standage3.9k
Davis, California, USA
Daniel Standage3.9k wrote:

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 &
repeats error • 4.4k views
ADD COMMENTlink modified 8 months ago by devarora230 • written 9.6 years ago by Daniel Standage3.9k
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).

ADD REPLYlink written 7.0 years ago by tflutre510

REPET is not easy to use and configure

ADD REPLYlink written 6 months ago by eennadi0

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

ADD REPLYlink written 7.5 years ago by jomaco190

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

ADD REPLYlink written 6.8 years ago by Rahul Sharma600

Same error, any ideas?

ADD REPLYlink written 6.6 years ago by Alex1.5k

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

ADD REPLYlink written 8 months ago by devarora230
1
gravatar for Buttonwood
6.5 years ago by
Buttonwood40
China
Buttonwood40 wrote:

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?

ADD COMMENTlink modified 12 months ago by RamRS30k • written 6.5 years ago by Buttonwood40
1
gravatar for Robert Hubley
5.4 years ago by
Robert Hubley10 wrote:

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

 

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Robert Hubley10
1
gravatar for WDbakker
2.2 years ago by
WDbakker10
Belgium
WDbakker10 wrote:

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.

ADD COMMENTlink written 2.2 years ago by WDbakker10
0
gravatar for geruispring
6.1 years ago by
Pakistan
geruispring0 wrote:

RECON: eleredef failed. Exit code 768

What is the reason for the error?

ADD COMMENTlink written 6.1 years ago by geruispring0
0
gravatar for maxwhjohn1988
2.5 years ago by
maxwhjohn1988100
maxwhjohn1988100 wrote:

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.

ADD COMMENTlink written 2.5 years ago by maxwhjohn1988100

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

ADD REPLYlink written 2.4 years ago by teuntje.peeters0

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.

ADD REPLYlink written 2.1 years ago by maxwhjohn1988100
0
gravatar for michael.b.broe
2.4 years ago by
michael.b.broe0 wrote:

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.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by michael.b.broe0
0
gravatar for bioinfo17
2.1 years ago by
bioinfo1730
bioinfo1730 wrote:

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

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by bioinfo1730
0
gravatar for devarora
8 months ago by
devarora230
SouthKorea
devarora230 wrote:

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.

ADD COMMENTlink modified 8 months ago • written 8 months ago by devarora230
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