Post SHRiMP2 samtools rmdup problem

[KJam]

Hi All,

I've run an alignment through SHRiMP2 sing the following command:

gmapper-ls --qv-offset 28 -a NAMEc_1.fastq -2 NAMEc_2.fastq Ref.fasta > Out.sam

and ended up with a .sam file that was tiny (1.5Mb), but looked like a real sam file!

Head:
@HD VN:1.0 SO:unsorted
@SQ SN:TD024 LN:9531
@PG ID:gmapper VN:2.2.3 CL:gmapper-ls --qv-offset 28 -1 TD024c_1.fastq -2 TD024c_2.fastq TD024.fasta
HISEQ2000-05:3052CR4ACXX:4:1101:11320:15903 0 TD024 3680 250 88M * 0 0 CTACCAGTGGAGAGAGAGACCTGGGAACAGTGGTGGGATGACTACTGGCAAGTAACATGGATCCCAGAATGGGACTTTGTGTCTACCC MKNNOLLFKMONONNKLLJKMLNNONOOOMGIJDIHMHLLNONOOLNOOLOJJJKMMMKKKKKKJJJIHIIHIHIIIIIIA>FIKIII AS:i:755 Z0:i:29353 Z1:i:29353 NM:i:5

It goes through sorting and mapping of unpaired reads fine but then when I get to rmdup the core opens the reference and then exits without removing any reads or telling me the fraction of reads removed.
Has anyone else had this problem? I'm assuming it's somehow got rid of a bit of positional data?
Ps. there are definitely duplicates in there!!

Any help would be greatly appreciated!

Kat