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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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main::main::postProcessSearch: FastaDB::substr - Error index out of bounds! #102

Closed Biscuite-wzy closed 2 years ago

Biscuite-wzy commented 2 years ago

Hi oushujun, I met a mistake when I run LTR_retriever, as follows:

main::main::postProcessSearch: FastaDB::substr - Error index out of bounds! (SeqID=ptg001350l:494544..499602|LTR_IN, offset=5039, length=129 actualSeqLen=5059) at /home/lx/miniconda3/envs/RepeatMasker/bin/RepeatMasker line 6016.

I do not know how to resolve it, can you help me? I will appreciate if you help me.

Best regards!

oushujun commented 2 years ago

Hi @Biscuite-wzy, sorry I just saw your message. I searched and found something similar: https://github.com/Dfam-consortium/RepeatModeler/issues/28 and also here: http://repeatmasker.org/archived-news.html

You may need to update your repeatmasker. Please also make sure your genome have simple and short sequence names.

Best, Shujun

Biscuite-wzy commented 2 years ago

Dear teacher ou, Thank teacher for reply. I have resolved it after revising the sequence names,but I met another problem when I ran LTR_retriever, as follows. I checked LTR_FINDER that has identified LTR. I do not know what is wrong. Looking forward to teacher's reply. Best regards

ying

------------------ 原始邮件 ------------------ 发件人: "oushujun/LTR_retriever" @.>; 发送时间: 2021年8月7日(星期六) 晚上11:57 @.>; @.**@.>; 主题: Re: [oushujun/LTR_retriever] main::main::postProcessSearch: FastaDB::substr - Error index out of bounds! (#102)

Hi @Biscuite-wzy, sorry I just saw your message. I searched and found something similar: Dfam-consortium/RepeatModeler#28 and also here: http://repeatmasker.org/archived-news.html

You may need to update your repeatmasker. Please also make sure your genome have simple and short sequence names.

Best, Shujun

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oushujun commented 2 years ago

Hi Ying,

Please check other issues to find similar cases, otherwise open a new issue for the new problem. I'll close this one since the original problem is resolved.

Best, Shujun