Hello, I am trying to convert sam to bam and keep getting an error:

The input file must be coordinate sorted and must have gone through fixmates with the mate scoring option on.
[W::sam_read1] Parse error at line 1
[bam_flagstat_core] Truncated file? Continue anyway.

Before this I was doing PE Trimmomatics with following BWA - MEM. Here is my code. I would appreciate any help :( Thank you!

#!/bin/bash -x

INPATH=/dir/subdir
reference=/dir/refseq.fasta
cd /mnt/home/usr/tools/samtools-1.9
./samtools faidx $reference
cd $INPATH

for file in $INPATH/*.sam ;
do
        bname=$(basename $file ".sam")
        echo $bname
        echo file: $file
        bamfile=$INPATH/$bname".bam"
        namesort=$INPATH/$bname"_sorted.bam"
        fixmate=$INPATH/$bname"_sorted_fixmate.bam"
        positionsort=$INPATH/$bname"_sorted_fixmate_position.bam"
        markdup=$INPATH/$bname"_sorted_fixmate_position_markdup.bam"
        bai=$INPATH/$bname".bai"
        stats=$INPATH/$bname".txt"
        echo $bamfile $namesort $fixmate $positionsort $markdup
        cd /mnt/home/usr/tools/samtools-1.9

        ./samtools view -bT $reference $file > $bamfile
        ls -lh
        ./samtools sort -@ 12 -n $bamfile > $namesort
        ./samtools fixmate -m $namesort > $fixmate
        ./samtools sort -@ 12 $fixmate > $positionsort
        ./samtools markdup $positionsort > $markdup
        ./samtools index > $markdup
        ./samtools flagstat $markdup > $stats
done