update alignment bug

alignment/rnaseqalign.sh

@@ -69,8 +69,9 @@ else
     else
 	samtools view -1 --threads $SLURM_CPUS_ON_NODE -o output.bam out.sam
     fi
-    samtools sort -@ $SLURM_CPUS_ON_NODE -O BAM -n -o output.nsort.bam output.bam
+    samtools sort -@ $SLURM_CPUS_ON_NODE -O BAM -o ${pair_id}.bam output.bam
     java -jar $PICARD/picard.jar FixMateInformation ASSUME_SORTED=TRUE SORT_ORDER=coordinate ADD_MATE_CIGAR=TRUE I=output.nsort.bam O=${pair_id}.bam
+
 fi
 
 samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.bam