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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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Can't exec "-misschar" #84

Closed Qiuming1986 closed 3 years ago

Qiuming1986 commented 3 years ago

Can't exec "-misschar": No such file or directory at LTR_retriever-master/bin/cleanup.pl line 61. Use of uninitialized value $tandem in substitution (s///) at LTR_retriever-master/bin/cleanup.pl line 62.

The software has been installed, howerver the process of calculation has the issue. And the results are as follow: Wed Nov 11 00:36:01 CST 2020 Dependency checking: All passed! Wed Nov 11 00:36:14 CST 2020 LTR_retriever is starting from the Init step. Wed Nov 11 00:38:10 CST 2020 The longest sequence ID in the genome contains 48 characters, which is longer than the limit (15) Trying to reformat seq IDs... Attempt 1... Wed Nov 11 00:38:29 CST 2020 Seq ID conversion successful!

Wed Nov 11 00:38:29 CST 2020 Start to convert inputs... Total candidates: 114885 Total uniq candidates: 111063

Wed Nov 11 00:39:10 CST 2020 Module 1: Start to clean up candidates... Sequences with 10 missing bp or 0.8 missing data rate will be discarded. Sequences containing tandem repeats will be discarded.

Wed Nov 11 00:39:17 CST 2020 110948 clean candidates remained

Wed Nov 11 00:39:18 CST 2020 Modules 2-5: Start to analyze the structure of candidates... The terminal motif, TSD, boundary, orientation, age, and superfamily will be identified in this step.

Wed Nov 11 01:18:56 CST 2020 Intact LTR-RT found: 0

Wed Nov 11 01:18:56 CST 2020 No LTR-RT was found in your data.

Wed Nov 11 01:18:57 CST 2020 All analyses were finished!

oushujun commented 3 years ago

Hi @Qiuming1986 ,

To make sure the installation is correct, please test your LTR_retriever with this toy genome or other small plant genomes: https://github.com/oushujun/EDTA/tree/master/test

Best, Shujun

Qiuming1986 commented 3 years ago

Dear Shujun,

I'm sorry to disturb you. I could not resolve the problem of Can't exec "-misschar". According to you suggestion, I have made the test. As you said, the installation is not correct. However, I don't know which software is not correct. RepeatMasker, HMMER, BLAST+, CDHIT or perl module? I would be much grateful if you could help me.

oushujun commented 3 years ago

Hi @Qiuming1986,

I don't know neither...without proper error messages. Most likely Repeatmasker is not properly installed. In this case I would suggest simply create a new conda env and install LTR_retriever fresh.

Best, Shujun

oushujun commented 3 years ago

@Qiuming1986 have you resolve the issue? Thanks. -Shujun

oushujun commented 3 years ago

I am closing this thread for now. Please reopen it if your issue is not resolved. Thanks! - Shujun