bwa sampe [fread] Unexpected end of file

[GSbioinfo]

I am running follwoing commad to convert .sai output of bwa aln to sam file
bwa sampe ref.fa read1.sai read2.sai read1.fastq read2.fastq >read.sam
and I am getting following error.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[fread] Unexpected end of file
sam file has no sequences
When I use samse converted read1.sai and read2.sai to separte sam files it works fine.
I also to 50 sequences from read1.fastq and read2.fastq did alignment and converted to sam file using sampe it also worked.
I am not sure why I am getting this error.
Really appreciate any help.
Thanks