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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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LTR Structural Analysis issue #60

Open Tdanis opened 4 years ago

Tdanis commented 4 years ago

Hello again, so could you help me with one issue with LTR_struct?

############### Running LtrHarvest... : 00:39:33 (hh:mm:ss) Elapsed Time Running Ltr_retriever...LTRPipeline: No results after LTR_Retriever filtering. LTRPipeline Time: 00:39:38 (hh:mm:ss) Elapsed Time

So, I took the above result in my output file, and at the end there are lots of LTRs into the consensi.fa.classified. Is it ok ? or there are problems during running?

LTR_retriever log file:

For LTR_retriever, please cite:

Ou S and Jiang N (2018). LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiol. 176(2): 1410-1422.

For LAI, please cite:

Ou S, Chen J, Jiang N (2018). Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 2018;46(21):e126.

Parameters: -genome seq.fa -inharvest /mnt/scratch/tdanis/RepeatModeler/Default/new/RM_34762.ThuJan231608202020/LTR_75226.FriJan241532132020/raw-struct-results.txt -noanno -threads 8

Fri Jan 24 16:11:46 EET 2020 Dependency checking: The RMblast engine is not installed in RepeatMasker!

Thank you for your time

jebrosen commented 4 years ago

Hello, sorry to hear you are having trouble with this.

Fri Jan 24 16:11:46 EET 2020 Dependency checking: The RMblast engine is not installed in RepeatMasker!

How did you install LTR_retriever? Make sure you have set the RepeatMasker= path as described in https://github.com/oushujun/LTR_retriever/#standard-installation . Also, when you configure RepeatMasker you must configure the RMBlast search engine so that LTR_retriever can use it.