build_lmer_table failed. Exit code 65280

[chhhhai]

Describe the issue

The software raises error ‘’build_lmer_table failed. Exit code 65280“，how to solve it？thanks for your help！！！

running log
(earlGrey) [aich@admin Repeat]$ RepeatModeler -database sesame -LTRStruct
WARNING: RepeatModeler is a computationally intensive program.
It is recommended that for anything other than debugging
purposes the program should run with greater than eight
threads (-threads #).

RepeatModeler Version 2.0.4

Using output directory = /home/aich/01.comparative_genomics/03.gene_class_test_data/genomics_training/42.GeneStructureAnnotation/Repeat/RM_66603.WedOct180604252023
Search Engine = rmblast 2.13.0+
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4
LTR Structural Analysis: Enabled ( GenomeTools 1.6.2, LTR_Retriever ,
Ninja /home/aich/01.comparative_genomics/03.gene_class_test_data/genomics_training/42.GeneStructureAnnotation/Repeat/sesame, MAFFT 7.520,
CD-HIT 4.8.1 )
Random Number Seed: 1697580260
Database = /home/aich/01.comparative_genomics/03.gene_class_test_data/genomics_training/42.GeneStructureAnnotation/Repeat/sesame

• Sequences = 1
• Bases = 18577331
  Storage Throughput = excellent ( 1223.87 MB/s )

Ready to start the sampling process.
INFO: The runtime of RepeatModeler heavily depends on the quality of the assembly
and the repetitive content of the sequences. It is not imperative
that RepeatModeler completes all rounds in order to obtain useful
results. At the completion of each round, the files ( consensi.fa, and
families.stk ) found in:
/home/aich/01.comparative_genomics/03.gene_class_test_data/genomics_training/42.GeneStructureAnnotation/Repeat/RM_66603.WedOct180604252023/
will contain all results produced thus far. These files may be
manually copied and run through RepeatClassifier should the program
be terminated early.

RepeatModeler Round # 1

Searching for Repeats
-- Sampling from the database...

• Gathering up to 40000000 bp
• Final Sample Size = 18577243 bp ( 18353842 non ambiguous )
• Num Contigs Represented = 1
• Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time
  -- Running RepeatScout on the sequences...
• RepeatScout: Running build_lmer_table ( l = 14 )..
  build_lmer_table failed. Exit code 65280

[rmhubley]

Could you try running the RepeatScout tool on your file directly like so:

<RSCOUT_INSTALL_DIR>/build_lmer_table -l 14 -sequence /home/aich/01.comparative_genomics/03.gene_class_test_data/genomics_training/42.GeneStructureAnnotation/Repeat/sesame -freq freq.out

And let me know what you get. Also I would recommend upgrading to RepeatModeler 2.0.5 and RMBlast 2.14.1

[chhhhai]

Could you try running the RepeatScout tool on your file directly like so:

<RSCOUT_INSTALL_DIR>/build_lmer_table -l 14 -sequence /home/aich/01.comparative_genomics/03.gene_class_test_data/genomics_training/42.GeneStructureAnnotation/Repeat/sesame -freq freq.out

And let me know what you get. Also I would recommend upgrading to RepeatModeler 2.0.5 and RMBlast 2.14.1
This is my previous command lines:

BuildDatabase -name sesame ../test_data/genome.fasta
RepeatModeler -database sesame  -LTRStruct

after your advice,I run this command lines:

/public/project/ACH20231007Comparative_Genomics_Analysis/01.comparative_genomics/03.earlgrey/RepeatScout-1.0.6/build_lmer_table -l 14 -sequence sesame -freq freq.out

it's not ok, than I change my command to get the freq.out, it seem to be ok, I feel strange.

/public/project/ACH20231007Comparative_Genomics_Analysis/01.comparative_genomics/03.earlgrey/RepeatScout-1.0.6/build_lmer_table -l 14 -sequence ../test_data/genome.fasta -freq freq.out

freq.zip