use File::chdir;
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Did you read the documentation for this module?    You are not using it anywhere in this program.

chdir '$dir/Hsapiens_fasta_folder';
...
chdir '$dir/targetp-1.1';
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You should verify that these functions worked correctly:

chdir '$dir/Hsapiens_fasta_folder' or warn "Cannot chdir to '$dir/Hsap
+iens_fasta_folder' because: $!";
...
chdir '$dir/targetp-1.1' or warn "Cannot chdir to '$dir/targetp-1.1' b
+ecause: $!";
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