Comments (5)
oushujun
commented on June 15, 2024
The first error is saying that your specified thread number is more than the thread number in your server. Others are a minor/non-harmful bug caused by fragmented input sequence.
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yuanhelianyi
commented on June 15, 2024
How to solve the problem caused by the fragmented input sequence?
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oushujun
commented on June 15, 2024
It seems that only one LTR candidate is affected by this issue, so you may just ignore it by now. I will push a bug fix in the next update.
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yuanhelianyi
commented on June 15, 2024
Thank you very much. I want to confirm wether the one LTR candidate indicate the retrotransposons with only one LTR, ie.,the solo-LTR or not. I found many lines of the error in my out file.
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oushujun
commented on June 15, 2024
Probably not. LTR_retriever is not designed to identify solo-LTRs. All input candidates should have a pair of long terminal-repeat.
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Related Issues (20)
- Invalid value for shared scalar HOT 10
- awk: fatal: cannot open file `genome.fa.mod.retriever.scn.extend.fa.rexdb.cls.tsv' for reading (No such file or directory) HOT 1
- awk: cannot open N02.fa.retriever.scn.extend.fa.rexdb.cls.tsv HOT 5
- ERROR: No candidate is found in the file(s) you specified. HOT 10
- LOC list New_genome.nextpolish.exceptChl.FINAL.fa.retriever.scn.full is empty HOT 3
- an error in Calculate LAI from EDTA HOT 2
- fa.mod.nmtf.pass.list is empty HOT 2
- LTR_retriever failed to generate a file - data passing in a multithreaded run HOT 2
- Are there any changes in Module 1 between versions 2.9.0 and 2.9.9? HOT 2
- cleanup.pl Bug? HOT 3
- same bug before about LTR.identifier.pl HOT 3
- A reviewer's comment related to the setting of mutaion rate HOT 2
- The LTR_retriever fails to identify LTRs with tandem repeats, such as Dasheng. HOT 3
- Dependency checker looking in wrong directory for makeblastdb HOT 1
- Assessing Chrysanthemum lavandulifolium genome assembly HOT 2
- Exploring the transposition profile of specific LTRs HOT 2
- LTR retriever is not compatible with RepeatModeler2 since v2.9.8? HOT 5
- Kimura2Paramter to ks value/Time HOT 2
- Calculated LAI is too large HOT 3
- LTR_retriever produce different result in different data combine ways
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