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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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Solved: Can't exec "-misschar" #100

Closed timkahlke closed 2 years ago

timkahlke commented 3 years ago

Hi,

I had the same problem as described in #84 and #91 . The reason is a missing Tandem Repeat Finder(trf) or, in case of #91 wrong permissions to execute it.

The weird error message comes from calling cleanup.pl with an empty -trf_path option which then sets $trf_path to the next index of @ARGV, i.e. -misschar. Adding the check and $ARGV[$k+1]!~/^-/ to each line in the foreach @ARGV block in cleanup.pl (as done in the other scripts) will change the error message to a meaningful can't execute /.../trf409.legacylinux64. No such file or directory.

oushujun commented 3 years ago

That's a good point. I will add this check to the next update. Thanks for the suggestion. - Shujun