I am running following command to convert paired end .sai output of bwa aln to one 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
and sam file has headers but no sequences When I use samse to convert read1.sai and read2.sai into separate read1.sam and read2.sam files it works fine. I also tested for first 50 sequences from read1.fastq and read2.fastq and did alignment and converted to sam file using sampe it also worked. So I am not sure why I am getting this error. Really appreciate any help. Thanks