Cufflinks Error: sort order of reads in BAMs must be the same I am running Cufflinks for transcriptome assembly using the .bam file generated by Hisat2. I tried both bam and sorted bam files

cufflinks --no-update-check -o ./ -p 15 accepted_hits.bam


it gives the following error:

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


UPDATE: It is working fine now. It seems there were some issues with the reference file. The BAM files generated from Tophat2 also gave the same error. I downloaded the updated reference file and it worked great.
Just add --dta-cufflinks to your Hisat2 command, so that the output alignment file provides the attributes needed by Cufflinks (XS flags). This should do the job.  

From manual:


  Report alignments tailored specifically for Cufflinks. In addition to
  what HISAT2 does with the above option (--dta), With this option,
  HISAT2 looks for novel splice sites with three signals (GT/AG, GC/AG,
  AT/AC), but all user-provided splice sites are used irrespective of
  their signals. HISAT2 produces an optional field, XS:A:[+-], for every
  spliced alignment.