RepeatModeler - Everything works except LTR Harvest

[NicMAlexandre]

Hello,

I have been running RepeatModeler on my de novo assembled genome. I have run it multiple times and it runs for about 4-5 days and completes with the expected consensi.fa.classified output file. However, the LTR run, which should generate another fasta in a separate folder, outputs the following:

LTR Structural Analysis

Running LtrHarvest...LtrPipeline: GenomeTools failed to build suffixtree datastructure. This is frequently caused by a lack of disk space. Error code: 65536 LTRPipeline: No results returned from LTR structural finder ( LtrHarvest ). LTRPipeline Time: 00:00:21 (hh:mm:ss) Elapsed Time I have ran on larger nodes and set the tmp directory to a location with unlimited space.

1. Has anyone encountered this error before and how did they resolve it?
2. Is there a way I can run LTR Harvest separately from the RepeatModeler run so I don't have to wait 4 days for a result?

I posted the above on biostars as well but have not gotten a response yet:

https://www.biostars.org/p/469504/

[jebrosen]

Has anyone encountered this error before and how did they resolve it?

As the error message suggests, how much free disk space is there? Can you run this command: find RM_directory_with_date -name suffixerator.log and post the contents of the file it lists?

Is there a way I can run LTR Harvest separately from the RepeatModeler run so I don't have to wait 4 days for a result?

Yes, LTRPipeline can be run separately (LTRPipeline genome.fa). Optionally you can use the -debug flag to keep more output and log files. Running LTRPipeline separately is mainly useful for troubleshooting, since it is not easy to combine with the traditional RepeatScout/RECON runs after the fact (that is issue #65).

[WeichenZhou]

Hi @jebrosen

I guess I have the same issue regarding the LTR Harvest. Running on the Slurm HPC and I don't think it has the disk space problem.

Could you please help with it?

Thank you so much!! Arthur