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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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Running Ltr_retriever...Died at /app/RepeatModeler-2.0.4/LTRPipeline line 693. #148

Closed ShirelyI closed 1 year ago

ShirelyI commented 1 year ago

Dear shujun: Thanks for your software.I met some wrong messages when I ran repeatmodeler,the log is as follows :

LTR Structural Analysis

Running LtrHarvest... : 00:00:09 (hh:mm:ss) Elapsed Time Running Ltr_retriever...Died at /biodb/labs/liuhuanzhang/app/RepeatModeler-2.0.4/LTRPipeline line 693. LTRPipeline Time: 00:02:09 (hh:mm:ss) Elapsed Time

Software were install manually :LTR_retriever-2.9.0 , RepeatModeler-2.0.4 , rmblast-2.13.0 , genometools-1.6.2 . The results compare to normal Ltr_retriever running were different. If I run Ltr_retriever seperately ,I'm not sure which file should be the inputfile after -inharvest? I tried to find solutions but found no answers.Could you please help me with this question? Looking forward to your reply. Best wishes, Lily

oushujun commented 1 year ago

Seems like this is a repeatmodeler2 issue. Please refer to the LTR_retrieve documentation regarding the input files.

Best, Shujun

ShirelyI commented 1 year ago

Hi Shujun, Ltr_retriever was installed by conda before, it works after manually installed . Thanks for your reply. Best wishes, Lily