Died at LTRPipeline line 693.

[minglibio]

Describe the issue

I am running the RepeatModeler on a ~900 Mb fish genome. The job was completed successfully and I got the families.fa and families.stk files. But at the same time I also got the following in the error output file:

Died at /path/to/RepeatModeler/LTRPipeline line 693.

Should I worry about this message?

Reproduction steps

1. Steps to reproduce the behavior, including the command lines given to the program

BuildDatabase -engine rmblast -name asm /path/to/asm/asm.fasta
RepeatModeler -database asm -LTRStruct -pa 4 

• and links to publicly available genome assemblies and other data files (if available).

Log output

Attached please find the log output. run.log

Environment (please include as much of the following information as you can find out):

• How did you install RepeatModeler? e.g. manual installation from repeatmasker.org, bioconda, the Dfam TE Tools container, or as part of another bioinformatics tool?

  RepeatModeler was installed by bioconda

• Which version of RepeatModeler do you have? The output of RepeatModeler without any options will be a help page with the version of the program displayed at the top.

  RepeatModeler - 2.0.3

• Which version of RepeatMasker is this RepeatModeler installation using? Have you installed RepBase RepeatMasker Edition for RepeatMasker, or the full Dfam database?

  RepeatMasker - 4.1.2-p1

• Operating system and version. The output of uname -a and lsb_release -a can be used to find this.

Additional context

• Add any other context you have about the problem here. Some possible examples:
  • If an older version of RepeatModeler worked before
  • If the problem only happens with specific data files

[minglibio]

I found it might be caused by the LTRPipeline can't find the RMblast engine:

Dependency checking: Error: The RMblast engine is not installed in RepeatMasker!

Strangely, when I run it locally, everything is fine. But when I use the task queue system (qsub) I get this error every time.

[SAMtoBAM]

I have the same issue. Did you figure out how to solve this issue?

[minglibio]

Hi @SAMtoBAM You can try to downgrade your RMblast. Version 2.10 works for me

[TymekPieszko]

Is there another explanation for this issue? I'm currently running RepeatModeler on two datasets, and get the message for one but not the other...

[ShirelyI]

Hi, I met the same issue , I tried to downgrade the version of rmblast but not works for repeatmodeler require rmblast2.13 or higher.Did you guys solve it ?