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do {
    ++$element2;
} until (substr($contigfile[$element2], 0, 1) eq '>');

perl -we 'do { print "hello\n" } until substr( undef, 0, 1 ) eq ">"'
hello
Use of uninitialized value in substr at -e line 1.
...
Use of uninitialized value in substr at -e line 1.
hello
...