Bfast Match Paired End Reads - Reports Half Total Number Of Reads

I'm using bfast 0.7.0a and testing on the paired end data present in the bfast user manual (Figure 5.4 in bfast-book.pdf). The format for this fastq file is shown that paired reads should follow sequentially in the file (read1R1, read1R2, read2R1, read2R2, etc). The same name is to be used for the sequential reads in a pair. So, the user manual data has 4 reads = two pairs. When I run bfast match:bfast match -A 0 -t -n 16 -f hg19.fa -i 1 -r bfast_book.fastq ************************************************************ Checking input parameters supplied by the user ... Validating fastaFileName hg19.fa. Validating readsFileName bfast_book.fastq. Validating tmpDir path ./. **** Input arguments look good! ************************************************************ ************************************************************ Printing Program Parameters: programMode: [ExecuteProgram] fastaFileName: hg19.fa mainIndexes 1 secondaryIndexes [Not Using] readsFileName: bfast_book.fastq offsets: [Using All] loadAllIndexes: [Not Using] compression: [Not Using] space: [NT Space] startReadNum: 1 endReadNum: 2147483647 keySize: [Not Using] maxKe ...