samtools pileup GLF

[phalaenopsis]

Hi,

I work with multiple bam-files which I have

1. merged (using samtools merge)
2. sorted (using samtools sort)
3. removed duplicates (using samtools rmdup)
4. sorted (using samtools sort)

I tried then to generate a GLF file
(using samtools -g -f reference.fasta merged_file.bam > merged_file.glf).
Samtools is running and generates GLF-files but before it stops, it throws out the following message
'[bam_pileup_core] the input is not sorted (chromosomes out of order)'
although the infile was sorted before (however, the bam-header flag was still set to 'unsorted')

I am really confused as samtools does not abort the pileup and I get an output GLF-file (I just don't know whether it is right or not....)

Thanks for your help!