Question: RepeatModeler finishes without creating output files
1
gravatar for Dave Carlson
3.0 years ago by
Dave Carlson90
Stony Brook University, NY
Dave Carlson90 wrote:

Hi All,

I am running RepeatModeler on a ~300 mb plant genome assembly to annotate transposable elements. The program successfully runs without error but it doesn't produce the "consensi.fa.classified" output file, and the "consensi.fa" file is empty. I find it highly unlikely that my genome assembly does not actually contain any repeats, so I'm confused about why this would happen. Anybody encountered this before or have any suggestions? Thanks! Dave

repeatmodeler • 1.5k views
ADD COMMENTlink written 3.0 years ago by Dave Carlson90
2

Have you tried running a test/small dataset to see if the program is correctly installed and performs as expected?

ADD REPLYlink written 3.0 years ago by genomax68k

Good idea. I just ran RepeatModeler on a small subset of my data, and it worked properly, producing all the appropriate output files.

ADD REPLYlink written 3.0 years ago by Dave Carlson90
1

That is a good sign that the software is correctly installed.

Now you need to figure out why the larger set fails. Make sure you are capturing stdout/stderr to files (or look at job scheduler logs if you are using one) since they may contain some clues.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax68k

Thanks. I'm running it again, specifically writing stdout/stderr to file this time. Hopefully if things still don't work properly, I'll have more info this time. Appreciate the suggestions!

ADD REPLYlink written 3.0 years ago by Dave Carlson90

Hello Dave !

I'm currently facing the exact same issue you had... Do you solved your issue ? I would like to know !

Cheers,

Roxane

ADD REPLYlink written 2.3 years ago by Roxane Boyer950

Hallo Roxane,

I am running into the same problem as well; I'll let you know if I find a way to fix it.

Cheers, Fabian

ADD REPLYlink written 2.3 years ago by Fabian0
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