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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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RepeatMasker: line 28: 25891 Segmentation fault #52

Closed zhaoruolan closed 4 years ago

zhaoruolan commented 4 years ago

(LTR_retriever) [00:07:33]rzhao@magnus-2:~/LTR_retriever$ 'LTR_retriever -genome /scratch/pawsey0149/rzhao/wheatProject/LTR_file/refKA_polished/refKA_polished.fasta'

##########################

LTR_retriever v2.6

##########################

Contributors: Shujun Ou, Ning Jiang

For LTR_retriever, please cite:

Ou S and Jiang N (2018). LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiol. 176(2): 1410-1422.

For LAI, please cite:

Ou S, Chen J, Jiang N (2018). Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 2018;46(21):e126.

Parameters: -genome /scratch/pawsey0149/rzhao/wheatProject/LTR_file/refKA_polished/refKA_polished.fasta

Fri Aug 23 00:14:17 AWST 2019 Dependency checking: The RMblast engine is not installed in RepeatMasker!

I checked the RepeatMasker library, the taxonomy.dat is not zipped.

Then I got the following message after running 'RepeatMasker -e ncbi -q -pa 1 -no_is -norna -nolow dummy060817.fa -lib dummy060817.fa'

group/pawsey0149/rzhao/anaconda/envs/LTR_retriever/bin/RepeatMasker: line 28: 25891 Segmentation fault (core dumped) perl /group/pawsey0149/rzhao/anaconda/envs/LTR_retriever/share/RepeatMasker/${NAME} $@

Do you know how to solve this problem?

Many thanks, Ruolan

oushujun commented 4 years ago

Dear Ruolan,

Please reinstall RepeatMasker either conda or manually. You may want to try this conda repository: conda install -c bioconda repeatmasker

Or try older versions of RepeatMasker available on conda: https://anaconda.org/bioconda/repeatmasker/files eg. conda install -c bioconda repeatmasker=4.0.8

Hope this helps!

Shujun

zhaoruolan commented 4 years ago

RepeatMasker Dear Shujun:

Problem solved! My supervisor told me to run ./configure under RepeatMasker. I followed the steps, then filled in the paths under LTR_retriever with the paths of those modules. Now I can pass the dependency check.

Many thanks, Ruolan