The read files are on the cluster server-as far as I know, I am not using an NFS share. I'm running the following (so I don't think I'm piping to samtools-I am outputting a sam file directly):

bwa mem -t 24 $ref $i.fastqsanger > $i.sam
done

then I plan to run the following:

# SAM to BAM, with read group information
for i in {21..30}; do
    picard AddOrReplaceReadGroups \
                I=$i.sam \
                O=$i.bam \
                RGID=4 \
                RGLB=lib1 \
                RGPL=pacbio \
                RGPU=unit1 \
                RGSM=anna
done

for i in {21..30}; do
        samtools sort $i.bam -o $i.sort.bam
    samtools index $i.sort.bam
done

# Samtools Merge
samtools merge all_runs.bam *.sort.bam

# Mpileup
bcftools mpileup -Ou -f $ref \