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.
Thank you for your work.
LAI did not run correctly.While running I get the following error $genome.tbl: No such file or directory
After checking I found out that it is due to the permissions of the $genome file.After runing RepeatMasker -e ncbi -pa $threads -q -no_is -norna -nolow -div 40 -lib $genome.LTRlib.fa -cutoff 225 $genome i got this error.
analyzing file $genome
FastaDB::_cleanIndexAndCompact() - Error could not open file ../LTR/RM_166328.TueMay32136282022/$genome: Permission denied
at /miniconda3/envs/lai/bin/RepeatMasker line 739.
and after chmod +w $genome , everything runs correctly
Thank you for your work. LAI did not run correctly.While running I get the following error
$genome.tbl: No such file or directoryAfter checking I found out that it is due to the permissions of the $genome file.After runingRepeatMasker -e ncbi -pa $threads -q -no_is -norna -nolow -div 40 -lib $genome.LTRlib.fa -cutoff 225 $genomei got this error.and after
chmod +w $genome, everything runs correctlyI add two line to check if $genome is writable.