LTRPipeline : Error - could not open clusters.dat!

[yasutoishii]

Hello,

Thank you for maintaining the useful tools. I encountered an error when I ran RepeatModeler to generate species-specific library for masking a de novo assembly.

Describe the bug The error was

Clustering...LTRPipeline: Error - could not cluster MAFFT results.
             : 00:00:00 (hh:mm:ss) Elapsed Time
LTRPipeline : Error - could not open /work/RM_13.SatJun290653562024/LTR_1007365.SunJun300251312024/clusters.dat! at /opt/RepeatModeler/LTRPipeline line 333.

To Reproduce The command was:

SCAFFOLD_FASTA=out_JBAT.FINAL.fa    ### My assembly file
PREFIX=scaffold
BuildDatabase -name ${PREFIX} ${SCAFFOLD_FASTA}
RepeatModeler -database ${PREFIX} -LTRStruct -threads 40

I mounted my local dir on /work with following command:

sudo docker run -it --rm -v $(pwd):/work dfam/tetools:latest

Host system (please complete as much of the following information as you can find out):

• My OS is: Ubuntu 20.04.6 LTS
• Docker info: Docker version 24.0.2, build cb74dfc
• Docker image: latest one created 4 months ago
• Computing environment setup: single computer

Additional context As the error said, I can't fine clusters.dat in /work/RM_13.SatJun290653562024/LTR_1007365.SunJun300251312024. The directory includes four files:

LtrRetriever-redundant-results.fa
LtrRetriever-redundant-results.fa.no_orient
mafft-alignment.fa
raw-struct-results.txt

Best, Yasuto

[kim2039]

This error is most likely caused by the NINJA version upgrade. If downloading from the URL of the latest release of NINJA and compiling it, it shows that it is actually downloading a 0.95 version, not 0.99. This has also been posted in an Issue of NINJA. https://github.com/TravisWheelerLab/NINJA/issues/46 I suggest using the older version of Ninja until this issue is resolved.

[yasutoishii]

Thanks Kim,

The version of NINJA was 0.95, as you mentioned. I tried tetools v. 1.8, but LTRpipeline provided another error:

Running LtrHarvest...LtrPipeline: GenomeTools failed to run ltrharvest. Error code: 139
LtrPipeline: Ltrharvest returned an unexpected result line:
Segmentation fault (core dumped)
LTRPipeline: No results returned from LTR structural finder ( LtrHarvest ).

I assume the cause is the shotage of RAM (my PC has ~ 200 GB RAM). I'll try it with more RAM!