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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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LTRHarvest Segmentation Fault #168

Open NicMAlexandre opened 2 years ago

NicMAlexandre commented 2 years ago

I have been running the most recent conda release of RepeatModeler which runs smoothly until round 6. The RepeatModeler job completes, but the LTR Structural Analysis never runs.

LTR Structural Analysis

Running LtrHarvest...sh: line 1: 244402 Segmentation fault /global/scratch/users/nalexandre/miniconda3/envs/repeat/bin/gt ltrharvest -index esa_index -out ltrharvest.out > ltrharvest.log 2>&1 LtrPipeline: GenomeTools failed to run ltrharvest. Error code: 139 LTRPipeline: No results returned from LTR structural finder ( LtrHarvest ). LTRPipeline Time: 36:22:12 (hh:mm:ss) Elapsed Time

The following are my commands:

conda create -n repeat source activate repeat conda install mamba mamba install -c bioconda repeatmasker repeatmodeler

wget https://github.com/TravisWheelerLab/NINJA/archive/0.95-cluster_only.tar.gz tar -xvzf 0.95-cluster_only.tar.gz

cp repbase.loach.fasta /global/scratch/users/nalexandre/miniconda3/envs/repeat/share/RepeatModeler/Libraries/RepeatMasker.Lib export TMPDIR=/global/scratch/users/faisalzaben/Loach/tmp

source activate repeat BuildDatabase -name Loach_Omnic omnic_loach.fasta RepeatModeler -database Loach_Omnic -pa 18 -LTRStruct -ninja_dir \ /global/scratch/users/faisalzaben/Loach/NINJA-0.95-cluster_only/NINJA -recoverDir RM_184364.FriMar180904562022

I use -recoverDir because I wanted to see if deleting the round 6 output and rerunning might result in LTR Harvest running.

The log output is empty.

kim2039 commented 2 years ago

I encountered the same bug. I am using it against a huge genome of axolotls. I have also been monitoring memory usage and it is fine. However, it is exiting with Error code 139. The logs are as follows;

LTR Structural Analysis

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 ). LTRPipeline Time: 196:38:38 (hh:mm:ss) Elapsed Time

RepeatClassifier Version 2.0.3

Search Engine = rmblast

  • Looking for Simple and Low Complexity sequences..
  • Looking for similarity to known repeat proteins..
  • Looking for similarity to known repeat consensi.. Classification Time: 00:44:04 (hh:mm:ss) Elapsed Time

Program Time: 217:51:26 (hh:mm:ss) Elapsed Time Working directory: /home/kim/SSD2/Axolotl/RepeatModeler/RM_779120.ThuMay190956212022 may be deleted unless there were problems with the run.

The results have been saved to: Axo-families.fa - Consensus sequences for each family identified. Axo-families.stk - Seed alignments for each family identified. Axo-rmod.log - Execution log. Useful for reproducing results.

The RepeatModeler stockholm file is formatted so that it can easily be submitted to the Dfam database. Please consider contributing curated families to this open database and be a part of this growing community resource. For more information contact help@dfam.org.

mkbcit commented 1 year ago

I have been running RepeatModeler2 in the Conda environment which runs smoothly until round 6. The RepeatModeler job completes, but the LTR Structural Analysis not return any results. Error return like:

LtrPipeline: GenomeTools failed to build suffixtree datastructure. This is frequently caused by a lack of disk space. Error code: 1