search

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
176 stars 40 forks source link

Something wrong with "-misschar" #78

Closed AntetokounmJie closed 3 years ago

AntetokounmJie commented 3 years ago

Hi, shujun I wanna use LAI to evaluate my genome assembly. And i do as you said here . When i pass all the depency checking, i got a error message like this: Can't exec "-misschar": No such file or directory at /my_paths_to/LTR_retriever/bin/cleanup.pl line 61. Use of uninitialized value $tandem in substitution (s///) at /my_paths_to/LTR_retriever/bin/cleanup.pl line 62.

But the ltr_retriever is still running. Mabye this message is not so important? Or can you tell me how to fix it? Thanks a lot.

AntetokounmJie commented 3 years ago

Hi, shujun I think i got the cause of this issue. In this cleanup.pl, the trf path is not rightly set here. I just replace the trf path with my absolute path in the cleanup.pl. And the error message is seemed to be gone. best regards

oushujun commented 3 years ago

Thanks for finding the issue. This script should not be affected because in LTR_retriever it has a check to make sure TRF is working and the path is passed to all associated scripts including cleanup.pl. Anyways, I have fixed the $trf path issue in cleanup.pl by adding an extra check and it will show in the next update.

Shujun

AntetokounmJie commented 3 years ago

Thanks for finding the issue. This script should not be affected because in LTR_retriever it has a check to make sure TRF is working and the path is passed to all associated scripts including cleanup.pl. Anyways, I have fixed the $trf path issue in cleanup.pl by adding an extra check and it will show in the next update.

Shujun

That`s great. :)