Error in Clustering Step of LTR Pipeline

[simone-says]

Describe the issue

Trying to run the LTR Pipeline alone to add to some libraries and then re-mask some genomes. So far, this is only happening with one genome. I use the -LTRStruc flag for RepeatModeler runs with no issues, not sure what the issue is here.

Reproduction steps

My exact commands are: srun apptainer exec --bind=/projects:/projects /common/contrib/containers/tetools-v1.88.sif LTRPipeline ${species_name}.genome.fa -threads 40

I don't know how to reproduce this exactly, I ran it twice when it failed and got the same error message. This is the genome that's giving an error: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_025583915.1/

Log output

Running LtrHarvest...     : 01:05:25 (hh:mm:ss) Elapsed Time
JANCLY010000001 is not in /projects/tollis_lab/busco_phylo/squamates/ref/omes/anolisSagrei.genome.fa.2bit
Running Ltr_retriever...  : 00:46:13 (hh:mm:ss) Elapsed Time
Aligning instances...     : 00:09:39 (hh:mm:ss) Elapsed Time
Clustering...LTRPipeline: Error - could not cluster MAFFT results.
             : 00:00:01 (hh:mm:ss) Elapsed Time
LTRPipeline : Error - could not open /projects/tollis_lab/busco_phylo/squamates/ref/omes/LTR_3321156.MonMar251237332024/clusters.dat! at /opt/RepeatModeler/LTRPipeline line 333.
srun: error: cn8: task 0: Exited with exit code 2

Environment (please include as much of the following information as you can find out): Using TETools apptainer on Slurm HPC

• 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? *TE Tools v1.88

• 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.

• Version 2.0.5

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

• RepeatMasker 4.1.6

• Operating system and version. The output of q and lsb_release -a can be used to find this. Linux wind 4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64 x86_64 x86_64 GNU/Linux

[rmhubley]

Sorry for the delay. If you still have these files, could you check that "JANCLY010000001" is in fact a sequence in your input file:

% fgrep JANCLY010000001 ${species_name}.genome.fa

and that it also occurs in the twobit file:

% twoBitInfo /projects/tollis_lab/busco_phylo/squamates/ref/omes/anolisSagrei.genome.fa.2bit stdout | grep JANCLY010000001

When I download the assembly from the link you provided (GCF_025583915.1_AnoSag2.1_genomic.fna.gz) I do not see a sequence named JANCLY010000001. Did you alter the assembly in any way, or get it from a different source?