bwa mem -x pacbio assembly.fa PacBio_raw.fastq > aln.sam

samtools view -b -S aln.sam -o aln.bam

samtools sort aln.bam > aln_sorted.bam

java -jar /share/apps/picard-tools-1.56/MarkDuplicates.jar INPUT=aln_sorted.bam METRICS_FILE=metricsFile CREATE_INDEX=true OUTPUT=alignments_markeddup.bam

This the command line for creating the alignment when am using picard for duplicates the metrics file producing is an empty file after this i will call the variants using the gatk any recommendations? thanks in advance