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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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LTR_Retriever RMBlast not installed #58

Closed RadeshNMP closed 4 years ago

RadeshNMP commented 4 years ago

Dear Shujun,

I am trying to run the LTR_Retriever to generate the LAI for a plant genome. When I tried to run the LTR_Retriever using the input of the LTR_harvest, I got the below error message regarding the RMblast.

Parameters: -genome /work/lianglab/wgs/lavender/LA_genome_final.fa -inharvest ../LA_ltrharvest_output -v

Wed Nov 6 15:04:36 EST 2019 Dependency checking: The RMblast engine is not installed in RepeatMasker!

I have run RepeatMasker before and I did not have any issues with it. Please let me know your thoughts and suggestions to get past this issue.

Thank you, Radesh

oushujun commented 4 years ago

Hi Radesh,

Sorry for the delay reply. This tells that the RepeatMasker does not have the -engine ncbi installed, which is RMblast. You may want to reinstall RepeatMasker or provide a version that has RMblast installed. The conda version v4.0.9_p2 works for me.

Best, Shujun

oushujun commented 4 years ago

43

oushujun commented 4 years ago

Closed due to inactivity. Please reopen it if you still have the issue.