I am trying to call variants from paired-read whole genome reseq data.  I have two fastq files (forward and reverse) for each sample.  I got to the MergeBamAlignment command and no matter what I try, I cannot get the file to generate.  The code itself runs in Linux, it is just my mergealignment.bam file never appears so I cannot proceed to the next step.  Does anyone have any advice?

Things I've tried: I've used ValidateSamFile to make sure all of my files have no errors and particularly making sure that the Read Groups were included at each stage.  I tried using RevertSam to revert my .sam files to unaligned files, however, I cannot get a RevertSam file to generate either.

a) GATK version used =4.0.3.0
b) Exact GATK commands used

#Generate the .sam files (one for each read direction)

../scripts/Read_Mapping_softwares/bwa/bwa mem -M -t 40 ../scripts/Read_Mapping_softwares/ref_bwa/Sbicolor_454_v3.0.1.fa read1.fq read2.fq > paired_aligned_reads_bwa_mem.sam

#The code below is where I can run the code but it does not generate the output file.

java -Xmx16G -jar picard.jar MergeBamAlignment ALIGNED=paired_aligned_reads_bwa_mem.sam UNMAPPED=unaligned_reads.bam O=paired_aligned_reads_mergebamalignment.bam R=../scripts/Read_Mapping_softwares/ref_bwa/Sbicolor_454_v3.0.1.fa CREATE_INDEX=true CLIP_ADAPTERS=false INCLUDE_SECONDARY_ALIGNMENTS=true MAX_INSERTIONS_OR_DELETIONS=-1 PRIMARY_ALIGNMENT_STRATEGY=BestMapq ATTRIBUTES_TO_RETAIN=XS CLIP_OVERLAPPING_READS=true