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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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ltrharvest issue #91

Open DNAcastigator opened 4 years ago

DNAcastigator commented 4 years ago

Good morning, I finally managed to install everything and the tool run to the end. Unfortunately, I'm having some issues with the LTRstruct pipeline: I run repeat Modeler on three different genomes and always got this error:

LtrPipeline: GenomeTools failed to run ltrharvest. Error code: 65536 LtrPipeline: Ltrharvest returned an unexpected result line: cannot flock: Function not implemented

and the final part of the output is this:

LTR Structural Analysis

Running LtrHarvest...LTRPipeline: No results returned from LTR structural finder ( LtrHarvest ). LTRPipeline Time: 00:05:06 (hh:mm:ss) Elapsed Time

RepeatClassifier Version 2.0.1

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: 00:19:54 (hh:mm:ss) Elapsed Time

Program Time: 56:53:48 (hh:mm:ss) Elapsed Time Working directory: /work/rpapa/aruggieri/RM/chari10/RM_58631.SatJul111029582020 may be deleted unless there were problems with the run.

The results have been saved to: /work/rpapa/aruggieri/RM/chari10/chari10-families.fa - Consensus sequences for each family identified. /work/rpapa/aruggieri/RM/chari10/chari10-families.stk - Seed alignments for each family identified.

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

I'm sorry to bother you again, but I couldn't find that error code anywhere. Another question: is it possible to run only the LTR pipeline without running again all RM ( because it takes around 50 hours to complete a run)

Thanks for your time

jebrosen commented 4 years ago

This looks like genometools/genometools#918, and the same workaround should apply.

Another question: is it possible to run only the LTR pipeline without running again all RM ( because it takes around 50 hours to complete a run)

Unfortunately no (see #65). Although you can "trick" RepeatModeler into starting from round 6 by renaming the file $recoverDir/round-6/consensi.fa so that it looks like a round that failed, and use the -recoverDir parameter.

yao-chenxin commented 4 years ago

RepeatModeler Version 2.0.1

Search Engine = rmblast 2.10.0+ Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.0 LTR Structural Analysis: Enabled ( GenomeTools 1.5.10, LTR_Retriever v2.8.7, Ninja 0.95-cluster_only, MAFFT , CD-HIT 4.8.1 ) why occur LTR Structural Analysis: Enabled？how to solution? Thank you !

jebrosen commented 4 years ago

@yao-chenxin LTR Structural Analysis: Enabled means that you have enabled the -LTRStruct option for RepeatModeler. If you do not want to include the LTR Structural Analysis, removing -LTRStruct from the command should work.