Cufflinks: sort order of reads in bams must be the same

[arabidopsis]

Hi all,

I am trying to run cufflinks on STAR-aligned reads. After converting to BAM and executing "sort" command I do this:

cufflinks -uN --GTF /path/to/reference.gtf -b /path/to/genome.fasta --compatible-hit-norm mapped_reads_sorted.bam

However, cufflinks does not run, reporting the following:
Error: sort order of reads in bams must be the same

This is double-confusing, because I am only using one BAM file...

Can someone help?

[eieneg]

Remove COLONS

Remove colons in the FASTA file and the GFF file.

[eieneg]

You must remove the colons in the FASTA reference and the GTF file. (make sure the names match up after)