Bowtie2 mapping message: [samopen] SAM header is present:

[struggler]

Dear All,

I am using Bowtie2 to map Illumina Hiseq reads to a reference genome and getting the following message:

[samopen] SAM header is present: 528 sequences

I don't know if this is a trivial issue or some significant error. I have tried searching details of this message but can't find any information on what does this '[samopen] SAM header is present:' line means and would highly appreciate some feedback on this message.

Regards,
S

[maubp]

It is a harmless bit of diagnostic information from samtools, but I would worry if your reference genome does not have 528 sequences.

[struggler]

Many thanks! Your reply is spot on as indeed the reference genome contains 528 fasta headers.

Regards,
S