unexpected BWA output when enabling multihit

[jorge]

Hello,

I have aligned with BWA and allowed a maximum of 100 multiple hits with this command:
bwa samse -n 100 database.fasta aln_sa.sai short_read.fastq > aln.sam

However the output file is not a sam file (see below) which I expected. Has anybody experience the same?

Thanks
Jorge

>SRR030012.5 100 30957
chr10 -126484170 0
chr3 -1113010 0
chr2 -232514635 0
chr16 -6430412 0
chr3 -115750401 0
chr8 -26092084 0
chr5 -89789506 0
chr1 -179320160 0
chr4 -80353991 0
chr1 -169779976 0
chr2 -57672668 0
chr6 -126943760 0
chr2 -115944596 0
chr16 -58665846 0
chr12 -77323712 0
chr12 -8541015 0
chr12 -75575699 0
chr3 -90117294 0
chr8 -20402676 0
chr15 -60835375 0
chr2 -231853752 0
chr2 -218080361 0
chr8 -137370420 0
chr21 -22766790 0
chr8 -112168254 0
chr4 -36842765 0
chr2 -79057663 0
chr2 -143434625 0
chrY -25246452 0
chr10 -1535935 0
chr2 -91704688 0
chr12 -112848359 0
chr3 -107334853 0
chr8 -111667999 0

[jorge]

Hi,

I found out I was using an old version of BWA, moving to the latest version gave me the expected sam file.

Jorge