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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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perl: symbol lookup error #59

Closed wuxiaopei0509 closed 4 years ago

wuxiaopei0509 commented 4 years ago

Hi,shujun When I use LTR_retriever to identify the LTR-RT derived from LTR-finder and LTR-harvest,it did not produce results what we want. I check the log file and found perl: symbol lookup error: /home/wuxiaopei/perl5/lib/perl5/x86_64-linux-thread-multi/auto/threads/threads.so: undefined symbol: Perl_Istack_sp_ptr Thu Nov 14 12:30:32 CST 2019 Intact LTR-RT found: 0

cp: cannot stat `luzhudujuan.fa.mod.retriever.scn.adj': No such file or directory Thu Nov 14 12:30:32 CST 2019 No LTR-RT was found in your data.

Thu Nov 14 12:30:32 CST 2019 All analyses were finished!

where is the problem?Can you help me?

oushujun commented 4 years ago

Hi, can you paste the complete log here? Thanks! -Shujun

On Thu, Nov 14, 2019, 1:01 AM wuxiaopei0509 notifications@github.com wrote:

Hi,shujun When I use LTR_retriever to identify the LTR-RT derived from LTR-finder and LTR-harvest,it did not produce results what we want. I check the log file and found perl: symbol lookup error: /home/wuxiaopei/perl5/lib/perl5/x86_64-linux-thread-multi/auto/threads/threads.so: undefined symbol: Perl_Istack_sp_ptr Thu Nov 14 12:30:32 CST 2019 Intact LTR-RT found: 0

cp: cannot stat `luzhudujuan.fa.mod.retriever.scn.adj': No such file or directory Thu Nov 14 12:30:32 CST 2019 No LTR-RT was found in your data.

Thu Nov 14 12:30:32 CST 2019 All analyses were finished!

where is the problem?Can you help me?

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oushujun commented 4 years ago

Hi @wuxiaopei0509 ,

From a google search, you may have mixed perl versions installed in your system. Ref: https://www.perlmonks.org/?node_id=832773 Please reinstall Perl using conda.

Best, Shujun

oushujun commented 4 years ago

Closed due to inactivity. Please reopen it if you still have the issue.

zillurbmb51 commented 4 years ago

Hello, I am having same problem. I removed perl using both yum and conda and then installed again using conda. But nothing happens. Any Help? Best, Zillur

wuxiaopei0509 commented 4 years ago

sorry , Zillur I have forgotten how to deal with it at last ,maybe you can install perl and LTR_retriever in the same conda env . Please create a new conda env and don't install in the base env . Best!