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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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the numbers and bps of all LTRs #66

Closed Dobkin-Sun closed 4 years ago

Dobkin-Sun commented 4 years ago

Dear Shujun,

Hello!Thanks for developing this software! I extracted 935179 LTRs , which have 1263197104 bps(~49.98%) in total. I got this result with ' .mod.out.gff' file. But I notice that the output files contain a file named '.mod.out.LTR.distribution.txt'. It tells me that the percentage of all LTRs in whole genome is 46.60%.So I want to know which result is reliable. And my result is from '.fasta' file not '.mod.fasta' with 'gff' file. So there is a problem if I am wrong? Any suggestions would be helpful.

Best Sun Daojin

oushujun commented 4 years ago

Dear Daojin,

Thank you for the report, there was a small bug when doing different counts, neither of these counts is accurate. I have fixed this bug in the new push.

Please rerun these two lines in your folder and you will get the consistent and updated result: perl $script_path/LTR_retriever/bin/LTR_sum.pl -genome $genome -all $genome.out > $genome.out.LTR.distribution.txt perl $script_path/LTR_retriever/bin/make_gff3_with_RMout.pl $genome.out

Best, Shujun

Dobkin-Sun commented 4 years ago

Dear Shujun, Thank you for replying! I have tried your new version "2.8.6". When I installed RepeatMasker ,it repoerted "Dependency checking: The RMblast engine is not installed in RepeatMasker!". But I solved this problem by install Text Soudex by CPAN. It seemed all right.But when I used the latest software, the last one of this workflow got stuck.I checked the output files.I only found the 'gff3' file and have not 'gff' file.I noticed that my CPU was occupied 100% in 48 hours and then the computer could not work.I have no choice but to reboot.So I want to know why the annotation process can not work. Best Sun Daojin

oushujun commented 4 years ago

Hi Daojin,

You don't need to reinstall the dependencies. By going into the LTR_retriever folder you can simply run git pull then the update is finished. To fix your current issue, you may run conda install -n LTR_retriever -c bioconda ltr-retriever.

Best, Shujun

Dobkin-Sun commented 4 years ago

Thanks a lot Dr Ou.