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Hi @oushujun,
Within the Dasheng LTR, there exists a tandem repeat, but according to the current filtering strategy of LTR_retriever, it seems to be filtered out. Below is a Dasheng LTR scn record …
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Dear Robert, Jeb and Francisco,
**Describe the issue**
I am working on a plant genome (~500Mb, het=1.29%). As the title mentioned, when I run RepeatModeler, LTR_retriever failed to generate a f…
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Dear LTR retriever developers,
I was using RepeatModeler and found that there is no output from LTR retriever (v2.9.8 and v.2.9.9, either from GitHub or Conda). This seems to have been reported be…
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I am running LTR Retriever as a part of RepeatModeler. RepeatModeler sets each dependency manually on the command line, including the -blastplus parameter. But LTR Retriever is looking in some other d…
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The version of LTR_retriever in this image is 2.9.0, but it appears the tool has been updated to 2.9.9. Would it be possible to update the image to include this recent update?
https://github.com/ou…
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Hi shujun ou,
Happy new year!
I have the same bug about LTR.identifier.pl(version 2.9.9), errors are listed below:
Invalid value for shared scalar at /public/home/zhangbo/mambaforge/envs/EDTA/sh…
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Dear Professor Zhang, @zhangrengang
I apologize for disturbing you in your busy schedule. I know that LTR_Retriever and TEsorter are paired together, but the author of LTR_Retriever, Shujun Ou, seem…
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When I run the test data, I meet some error. The log is following:
Fri May 31 15:04:06 CST 2024 EDTA_raw: Check dependencies, prepare working directories.
Fri May 31 15:04:07 CST 2024 Star…
wwenc updated
2 weeks ago
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Hi, I'm in the process of updating to 2.9.9 from 2.9.0 and I'm seeing some odd outputs:
```
~/projects/LTR_retriever$ ./LTR_retriever -genome dmel-smaller.fa -inharvest raw-struct-results.txt
###…
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$ perl ../EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice7.0.0.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 10 > EDTA.tes…