oushujun
commented
4 years ago Hello,
Looks like your perl is not correctly installed. Please reinstall perl on your conda env and try again.
Best, Shujun
On Wed, Jan 8, 2020, 10:40 PM zhangleigloria notifications@github.com wrote:
Hi Shujun， I installed LTR_retriever with conda quickly，and the following error occurred. Parameters: -genome niechi.genome.fasta -inharvest niechi.harvest.scn -infinder niechi.finder.scn -t 8
Thu Jan 9 12:10:31 CST 2020 Dependency checking: All passed! Thu Jan 9 12:11:16 CST 2020 LTR_retriever is starting from the Init step. Thu Jan 9 12:13:42 CST 2020 Start to convert inputs... Total candidates: 7568 Total uniq candidates: 7074
Thu Jan 9 12:15:40 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.
Thu Jan 9 12:17:27 CST 2020 4686 clean candidates remained
Thu Jan 9 12:17:27 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.
Can't locate object method "end" via package "Thread::Queue" at ./LTR_retriever/bin/LTR.identifier.pl line 125. Thu Jan 9 12:20:24 CST 2020 Intact LTR-RT found: 0
cp: cannot stat `niechi.genome.fasta.retriever.scn.adj': No such file or directory Thu Jan 9 12:20:24 CST 2020 No LTR-RT was found in your data.
Thu Jan 9 12:20:24 CST 2020 All analyses were finished!
Do you know why this problem occurs?Thank you very much!
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/oushujun/LTR_retriever/issues/61?email_source=notifications&email_token=ABNX4NHKY6R3MXL6FI3NTR3Q42TEXA5CNFSM4KESMCLKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IE6JJNQ, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NBSMGZB7M2C65TT27DQ42TEXANCNFSM4KESMCLA .
Hi Shujun， I installed LTR_retriever with conda quickly，and the following error occurred. Parameters: -genome niechi.genome.fasta -inharvest niechi.harvest.scn -infinder niechi.finder.scn -t 8
Thu Jan 9 12:10:31 CST 2020 Dependency checking: All passed! Thu Jan 9 12:11:16 CST 2020 LTR_retriever is starting from the Init step. Thu Jan 9 12:13:42 CST 2020 Start to convert inputs... Total candidates: 7568 Total uniq candidates: 7074
Thu Jan 9 12:15:40 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.
Thu Jan 9 12:17:27 CST 2020 4686 clean candidates remained
Thu Jan 9 12:17:27 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.
Can't locate object method "end" via package "Thread::Queue" at ./LTR_retriever/bin/LTR.identifier.pl line 125. Thu Jan 9 12:20:24 CST 2020 Intact LTR-RT found: 0
cp: cannot stat `niechi.genome.fasta.retriever.scn.adj': No such file or directory Thu Jan 9 12:20:24 CST 2020 No LTR-RT was found in your data.
Thu Jan 9 12:20:24 CST 2020 All analyses were finished!