Closed:StringTie error input file not sorted, even though it is

Question

[sg197]

I've been following the stringtie pipeline for differential expression. I'm up to the stage of stringtie -e -B where I'm using the merged transcript file with the alignment (.bam) files to get read coverage tables.

root="/mnt/fls01-home01/mfbx3sgh/scratch"   
file=$root/Genome/*.bam  

stringtie $file -p 8 -e -B --fr 
            -G $root/FPKM_count/stringtie_merged_samples.gtf

I keep getting the error "the input alignment file is not sorted". My bam alignment files are definitely co-ordinate sorted, and I used them in the first step of the pipeline to generate the transcript assemblies with no problems. Anyone had a similar problem?? Thanks