bowtie2 sam files problem

[cz0013]

I am having problems converting some sam files that I created using bowtie2. I created the files and when I went to convert them to bam files I was given the error message no @SQ lines in the header missing header abort. When I went to look at the files to see the header problem they were blank. All of the files except for the first one that was created had this problem. The first file however did work with out any problems. Does anyone know why this may have happened and how I could fix it.
Thanks

[dpryan]

Did you give the --no-hd parameter or something?

[cz0013]

Not that I know of should I have used that parameter?

[dpryan]

No, but that would have caused the headerless SAM file. Just specify a header file when you convert to BAM.

[cz0013]

I figured the problem out. I was running Bowtie2 in the background and for some reason it didn't like this. What I did was run Bowtie2 but before the command I put screen, so it wasn't running in the background. Then it worked fine.