Error: sort order of reads in BAMs must be the same I am a novice to bioinformatics trying to run a cuffdiff job in cufflinks and keep getting this error message: 

Error: sort order of reads in BAMs must be the same


GENERATING SAM FILES:

cd /fs/project/PMIU0157/Claire_Stoll/RNASeq/B73_hisat2/B73_hisat2_11-5
module load hisat2  
hisat2 -k 1 -p 8 -S 11-5_B73_accepted_hits.sam -x /fs/project/PMIU0157/Claire_Stoll/RNASeq/B73_hisat2/B73_Zea_mays.AGPv4.dna.toplevel -1 /fs/project/PMIU0157/Claire_Stoll/RNASeq/11-5_FCHHL7JBBXX_L7_DLPRMzP300H3AAAPEI-27_1.fq  -2 /fs/project/PMIU0157/Claire_Stoll/RNASeq/11-5_FCHHL7JBBXX_L7_DLPRMzP300H3AAAPEI-27_2.fq


cd /fs/project/PMIU0157/Claire_Stoll/RNASeq/Mo17_hisat2/Mo17_hisat2_11R-5
module load hisat2  
hisat2 -k 1 -p 8 -S 11-5_Mo17_accepted_hits.sam -x /fs/project/PMIU0157/Claire_Stoll/RNASeq/Mo17_hisat2//Mol17_Ref_Lai -1 /fs/project/PMIU0157/Claire_Stoll/RNASeq/11R-5_DLPRMzP300B4AAAPEI-2_1.fq  -2 /fs/project/PMIU0157/Claire_Stoll/RNASeq/11R-5_DLPRMzP300B4AAAPEI-2_2.fq


CONVERTING SAM TO BAM: 

cd /fs/project/PMIU0157/Claire_Stoll/RNASeq/B73_hisat2/B73_hisat2_11-5
module load samtools 
samtools view -bS a_B73_11-5_accepted_hits.sam &gt; a_B73_11-5_accepted_hits.bam
samtools sort a_B73_11-5_accepted_hits.bam -o a_B73_11-5_accepted_hits.sorted.bam

cd /fs/project/PMIU0157/Claire_Stoll/RNASeq/Mo17_hisat2/Mo17_hisat2_11-5
module load samtools 
samtools view -bS a_Mo17_11-5_accepted_hits.sam &gt; a_Mo17_11-5_accepted_hits.bam
samtools sort a_Mo17_11-5_accepted_hits.bam -o a_Mo17_11-5_accepted_hits.sorted.bam


CUFFDIFF JOB

cd /fs/project/PMIU0157/Claire_Stoll/RNASeq/B73_hisat2/B73_hisat2_11-5
module load cufflinks/2.2.1
cuffdiff -b /fs/project/PMIU0157/Claire_Stoll/RNASeq/B73_hisat2/B73_hisat2_11-5 -u -N -p 8 /fs/project/PMIU0157/Claire_Stoll/Zea_mays.AGPv4.36.chr.gff3 /fs/project/PMIU0157/Claire_Stoll/RNASeq/B73_hisat2/B73_hisat2_11-5/a_B73_11-5_accepted_hits.sorted.bam /fs/project/PMIU0157/Claire_Stoll/RNASeq/Mo17_hisat2/Mo17_hisat2_11-5/a_Mo17_11-5_accepted_hits.sorted.bam
I think cuffdiff is not quite giving you the right error...it looks like the crux of your problem is you aligned each sample to a different reference.