tried converting from .fa to br a reference sequence file. Each line is 169 characters long
in the FASTA file and the error can be seen below.
When each line was split in half, there was no error, and conversion from .fa to br completed fine.
See sample input file (partial file due to space restrictions)
java -Xmx2000M -jar ConvertFastaForCloud.jar gi_8331925.fasta gi_8331925.br
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 0