Multi-fasta files need to be formatted to have the heading and the data on one line to be passed to Hadoop Mappers.
There is a helper script in the library that can convert multi-fasta file to that format
>>> ./inputFormatter inputFile OutputFile
inputFile: multi-fasta file to format
outputFile: file to write the output to
Note
pass the formatted file as the tool input
Example 1
format sequences.fasta and write it in sequences.formatted
./inputFormatter sequences.fasta sequences.formatted