Off topic:Missing SAM header after SOAP alignment

Question

[fiona.newberry]

Hi,

I am using SOAPaligner and soap2sam.pl to convert the output file to a sam file.

I then try to convert the supposed sam file to a bam file and get this error messages

[E::sam_parse1] missing SAM header
[W::sam_read1] parse error at line 1
[main_samview] truncated file.

This is what the soap alignment file looks like:

simulated.A.A.1.2618103/1   TGGAACAACTATACCAAACCAATTCAAAACGAAGAACTAACATCTTTAATTAGAGGAGCACAAACAGCAATGGATCAAACCGCAGAAGAAGAAATGGACT    IIIIHHHIIGIHIGHIIIHFEHIGGFIIIIIIEEICIIIICIIGIIIIAIAHIBGE@DFIEI>EI;:E<IICIIIIIIIIIIII?D?F>IICIDBFF:II    1   a   100 +   gi|9627186|ref|NC_001539.1| 401 2   A->82C9 T->29C9 100M    29T52A17

And the what the sam file looks like after soap2sam:

simulated.A.A.1.2618103 99  gi|9627186|ref|NC_001539.1| 401 30  100M    =   568 267 TGGAACAACTATACCAAACCAATTCAAAACGAAGAACTAACATCTTTAATTAGAGGAGCACAAACAGCAATGGATCAAACCGCAGAAGAAGAAATGGACT    IIIIHHHIIGIHIGHIIIHFEHIGGFIIIIIIEEICIIIICIIGIIIIAIAHIBGE@DFIEI>EI;:E<IICIIIIIIIIIIII?D?F>IICIDBFF:II    NM:i:2  MD:Z:29T52A17

Obviously it is missing the normal lines you would see in sam file (@HD, @SQ, etc)

Does anyone know what is going on?