SUBJECT: Stampy software error with PairSorter

[megnat]

Hi all,
I am trying to map reads (Paired End) from a sample to a reference assembly that is somewhat divergenct (~3%). So I used the bam file after bwa mapping and tried to run that through stampy again as follows:
${STAMPY} -t30 -g athCun1_ens -h athCun1_ens --bamkeepgoodreads --bwamark --substitutionrate=0.03 --output=JO1.adaptersmarked.aligned.merged.ensembl.stampy-div3.sam -M JO1.adaptersmarked.aligned.merged.ensembl.bam
It created multiple bam and one sam file (I had listed sam as the output type, by extension). The output error file had an error in it (see below) but also the numbers of aligned reads (I think).
stampy: (PairSorter) 'samtools sort -o -n -m200000000 - JO1.adaptersmarked.aligned.merged.ensembl.stampy-div3.samec7b5a5b-5bec-4c39-9ab4-ce6e1f320c23' returned messages on stderr:
stampy: (PairSorter) (samtools ERROR) [bam_header_read] EOF marker is absent. The input is probably truncated.
stampy: (PairSorter) 'samtools view -h -' returned messages on stderr:
stampy: (PairSorter) (samtools ERROR) [bam_header_read] EOF marker is absent. The input is probably truncated.
stampy: # Nucleotides (all/1/2): 52813084200 26406542100 26406542100
stampy: # Variants: 3212191560 1458708466 1753483094
stampy: # Fraction: 0.0608 0.0552 0.0664
stampy: Done
However, when I checked the output sam file with samtools flagstat, it showed almost the same number (and percentage) of reads getting mapped. However, the proportion of properly paired reads went down a bit.
Would you know (a) what the error means and how to fix that? (b) Why I might be getting mapping where the proportion of paired reads decreases?
Thank you in advance!