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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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call_seq_by_list.pl uninitialized $chr_pre ? It will cause nagative start or end. #40

Closed YuntaoTan closed 5 years ago

YuntaoTan commented 5 years ago

Hi, oushujun, I use the Ltr_retriver find LTR based on LTR_finder and LTR haverst result. but I got the error: call_seq_by_list.pl uninitialized $chr_pre So I find the 84 line. Floowing I found, my $chr_pre=$1 if (split /\s+/, $list[0])[1]=~/(.*):-?[0-9]+\.\.[0-9]+$/; I anaysis the code , it may be cased by too short scaffold, when the program extend the sequence forward or backward. It will occur nagative start or end. I try to change the code to my $chr_pre=$1 if (split /\s+/, $list[0])[1]=~/(.*):-?[0-9]+\.\.-?[0-9]+$/; make it match the nagtive end. but failed, other Error I encountered. Can you help me ? How can i fix this Error?

oushujun commented 5 years ago

Hello @YuntaoTan ,

Thank you for using LTR_retriever. You may try to replace line 84 with: my $chr_pre=$1 if (split /\s+/, $list[0])[1]=~/(.*):[\-0-9]+\.\.[\-0-9]+$/; Let me know if this works or not.

If you have negative coordinates in the list, the bug may be inherited in former steps. Which step are you having this error? Can you paste the LTR_retriever status output here? A sample of the list file will be also helpful to track down the bug. Thanks!

Best, Shujun

oushujun commented 5 years ago

Close due to no response. Please reopen this issue if you have further questions.