LTRHarvest fails to run

[harish0201]

Describe the issue

I'm not sure if these are a singular problem or a series of problems. FWIW, I'm doing this on SLURM.

1. LtrPipeline: GenomeTools failed to run ltrharvest. Error code: 65536
2. LtrPipeline: Ltrharvest returned an unexpected result line:
3. cannot flock: No locks available
4. Results only the creation of genome index.

Reproduction steps

1. I'm using a large Bovine genome (~2.7Gb). You can check this from NCBI as well.
2. No other steps.

Log output

LTR Structural Analysis
=======================
Running LtrHarvest...LTRPipeline: No results returned from LTR structural finder ( LtrHarvest ).
LTRPipeline Time: 00:32:02 (hh:mm:ss) Elapsed Time

Results in an empty folder containing the index files from suffixerator

Environment (please include as much of the following information as you can find out): SLURM Workload Manager. RepeatModeler and Masker installed using conda. Ninja (clustering tool, not the compilation one, v0.95) has been installed manually and symlinked into the environments path.

• 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? Using Bioconda in a separate enviroment

• 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 version 2.0.1

• Which version of RepeatMasker is this RepeatModeler installation using? Have you installed RepBase RepeatMasker Edition for RepeatMasker, or the full Dfam database? Just the 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. uname -a : Linux master 5.4.0-66-generic #74~18.04.2-Ubuntu SMP Fri Feb 5 11:17:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux lsb_release -a: No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 18.04.3 LTS Release: 18.04 Codename: bionic

[jebrosen]

The root problem seems to be this:

cannot flock: No locks available

This is more likely to happen on a network filesystem and you did mention using SLURM; a local filesystem should not have such a problem with file locks. Do you have access to a local filesystem you could try, in case that resolves the issue?