These commands were used to generate bam files from fastq paired files. 

java -jar FastqToSam.jar FASTQ=/projects/redser/raw/150410_SW018_SW019_BananaSlug_HiSeq/SW019_S2_L008_R1_001.fastq.gz FASTQ2=/projects/redser/raw/150410_SW018_SW019_BananaSlug_HiSeq/SW019_S2_L008_R2_001.fastq.gz QUALITY_FORMAT=Standard OUTPUT=/scratch/bananaSlugBAMS/SW019_S2_L008_001.bam SAMPLE_NAME=SW019_S2_L008_001

java -jar FastqToSam.jar FASTQ=/projects/redser/raw/150410_SW018_SW019_BananaSlug_HiSeq/SW018_S1_L007_R1_001.fastq.gz FASTQ2=/projects/redser/raw/150410_SW018_SW019_BananaSlug_HiSeq/SW018_S1_L007_R2_001.fastq.gz QUALITY_FORMAT=Standard OUTPUT=/scratch/bananaSlugBAMS/SW018_S1_L007_001.bam SAMPLE_NAME=SW018_S1_L007_001 TMP_DIR=/scratch/tmp

java -jar FastqToSam.jar FASTQ=/projects/redser/raw/150311_M00160_0068_000000000-AAHYE/SW019_S1_L001_R1_001.fastq.gz FASTQ2=/projects/redser/raw/150311_M00160_0068_000000000-AAHYE/SW019_S1_L001_R2_001.fastq.gz QUALITY_FORMAT=Standard OUTPUT=/scratch/bananaSlugBAMS/SW019_S1_L001_001.bam SAMPLE_NAME=SW019_S1_L001_001