Running STAR on multiple replicates

I have 2 samples with 3 replicates each having PE reads. If I run:

STAR --genomeDir genomeDir/ 
    --readFilesIn Sample1-rep1-read1,sample1-rep2-read1,sample1-rep3-read1, sample1-rep1-read2,sample1-rep2-read2,sample1-rep3-read2 
    --runThreadN 8 
    --outSAMtype BAM SortedByCoordinate 
    --quantMode GeneCounts 

STAR --genomeDir genomeDir/ 
    --readFilesIn Sample2-rep1-read1,sample2-rep2-read1,sample2-rep3-read1, Sample2-rep1-read2,sample2-rep2-read2,sample2-rep3-read2
    --runThreadN 8 
    --outSAMtype BAM SortedByCoordinate 
    --quantMode GeneCounts

I get only this ouput in my ReadsPerGene.out.tab:

N_unmapped      1101143 1101143 1101143
N_multimapping  118148  118148  118148
N_noFeature     780486  2709783 2726521
N_ambiguous     0       0       0

Should I run a single star command on each read pair using a loop instead?