Missing SAM header after SOAP alignment
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?
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Wasn't this just answered in your last thread: SOAP aligner removes samfile headers
I am going to temporarily close this question until @fiona adds some clarification.
I tried what was in the last thread. Hence why I have posted a new one
If the answer did not work (from last thread) then you should edit that post and continue the conversation. Editing your previous post will bump it to front page.
Hello fiona.newberry!
Waiting clarification from @fiona
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!