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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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Use of uninitialized value $ac/$bd #33

Closed yuanhelianyi closed 5 years ago

yuanhelianyi commented 5 years ago

I am getting the following error while running v2.0. I don't know what caused it. Please help me. Error: Argument "num_threads". Illegal value, expected (>=1 and =<32): `40' Use of uninitialized value $bd in substitution (s///) at /data2/zhaoJing/bin/LTR_retriever-2.0/bin/LTR.identifier.pl line 301. Use of uninitialized value $ac in substitution (s///) at /data2/zhaoJing/bin/LTR_retriever-2.0/bin/LTR.identifier.pl line 300. Use of uninitialized value $ac in pattern match (m//) at /data2/zhaoJing/bin/LTR_retriever-2.0/bin/LTR.identifier.pl line 303. Use of uninitialized value $bd in pattern match (m//) at /data2/zhaoJing/bin/LTR_retriever-2.0/bin/LTR.identifier.pl line 303.

oushujun commented 5 years ago

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.

yuanhelianyi commented 5 years ago

How to solve the problem caused by the fragmented input sequence?

oushujun commented 5 years ago

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.

yuanhelianyi commented 5 years ago

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.

oushujun commented 5 years ago

Probably not. LTR_retriever is not designed to identify solo-LTRs. All input candidates should have a pair of long terminal-repeat.